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{ "count": 9394, "next": "?page=2", "previous": null, "list": [ { "name": "OmicsQ", "description": "OmicsQ is a Shiny-based web application designed for preprocessing and quantitative analysis of Omics data. It streamlines the preparation of data for subsequent analysis using specialized tools such as PolySTest for statistical testing and VSClust for clustering analysis.", "homepage": "https://computproteomics.bmb.sdu.dk/app_direct/OmicsQ/", "biotoolsID": "OmicsQ", "biotoolsCURIE": "biotools:OmicsQ", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3799", "term": "Quantification" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" }, { "uri": "http://edamontology.org/operation_2939", "term": "Principal component visualisation" }, { "uri": "http://edamontology.org/operation_3465", "term": "Correlation" }, { "uri": "http://edamontology.org/operation_4034", "term": "Multiple testing correction" }, { "uri": "http://edamontology.org/operation_0313", "term": "Expression profile clustering" }, { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" }, { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_0951", "term": "Statistical estimate score" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_3753", "term": "Over-representation data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] } ], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3391", "term": "Omics" } ], "operatingSystem": [], "language": [ "R", "JavaScript" ], "license": "Apache-2.0", "collectionID": [ "Proteomics" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Denmark" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/computproteomics/OmicsQ", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/computproteomics/OmicsQ/blob/main/www/tutorial/Tutorial.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.48550/ARXIV.2504.19813", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "veitveit11", "additionDate": "2025-07-02T09:38:59.620332Z", "lastUpdate": "2025-07-02T09:38:59.624571Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "RepeatModeler2", "description": "RepeatModeler is a de novo transposable element (TE) family identification and modeling package. At the heart of RepeatModeler are three de-novo repeat finding programs ( RECON, RepeatScout and LtrHarvest/Ltr_retriever ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data.", "homepage": "https://github.com/Dfam-consortium/RepeatModeler", "biotoolsID": "RepeatModeler2", "biotoolsCURIE": "biotools:RepeatModeler2", "version": [ "2.0.7" ], "otherID": [], "relation": [ { "biotoolsID": "repeatmodeler", "type": "isNewVersionOf" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0525", "term": "Genome assembly" }, { "uri": "http://edamontology.org/operation_3644", "term": "de Novo sequencing" }, { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_0157", "term": "Sequence composition, complexity and repeats" }, { "uri": "http://edamontology.org/topic_3673", "term": "Whole genome sequencing" }, { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_0798", "term": "Mobile genetic elements" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "Perl" ], "license": "OSL-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/Dfam-consortium/RepeatModeler/blob/master/LICENSE", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1101/856591", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "Pub2Tools", "additionDate": "2020-01-14T08:51:14Z", "lastUpdate": "2025-07-01T04:28:03.302129Z", "editPermission": { "type": "public", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Chopper", "description": "Rust implementation of NanoFilt+NanoLyse, both originally written in Python. This tool, intended for long read sequencing such as PacBio or ONT, filters and trims a fastq file.", "homepage": "https://github.com/wdecoster/chopper", "biotoolsID": "chopper", "biotoolsCURIE": "biotools:chopper", "version": [ "v0.10.0b" ], "otherID": [], "relation": [ { "biotoolsID": "nanopack", "type": "isNewVersionOf" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3695", "term": "Data filtering" }, { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "note": null, "cmd": "gunzip -c reads.fastq.gz | chopper -q 10 -l 500 | gzip > filtered_reads.fastq.gz\nchopper -q 10 -l 500 -i reads.fastq > filtered_reads.fastq\nchopper -q 10 -l 500 -i reads.fastq.gz | gzip > filtered_reads.fastq.gz" }, { "operation": [ { "uri": "http://edamontology.org/operation_2940", "term": "Scatter plot plotting" }, { "uri": "http://edamontology.org/operation_2943", "term": "Box-Whisker plot plotting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3579", "term": "JPG" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [], "license": "MIT", "collectionID": [ "ONTeater" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/wdecoster/chopper", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/bioinformatics/btad311", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "NanoPack2: population-scale evaluation of long-read sequencing data", "abstract": "Increases in the cohort size in long-read sequencing projects necessitate more efficient software for quality assessment and processing of sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Here, we describe novel tools for summarizing experiments, filtering datasets, visualizing phased alignments results, and updates to the NanoPack software suite. Availability and implementation: The cramino, chopper, kyber, and phasius tools are written in Rust and available as executable binaries without requiring installation or managing dependencies. Binaries build on musl are available for broad compatibility. NanoPlot and NanoComp are written in Python3. Links to the separate tools and their documentation can be found at https://github.com/wdecoster/nanopack. All tools are compatible with Linux, Mac OS, and the MS Windows Subsystem for Linux and are released under the MIT license. The repositories include test data, and the tools are continuously tested using GitHub Actions and can be installed with the conda dependency manager.", "date": "2023-05-01T00:00:00Z", "citationCount": 211, "authors": [ { "name": "De Coster W." }, { "name": "Rademakers R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Wouter de Coster", "email": "decosterwouter@gmail.com", "url": "https://gigabaseorgigabyte.wordpress.com", "orcidid": "https://orcid.org/0000-0002-5248-8197", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "Keiler_Collier", "additionDate": "2025-06-18T09:20:19.874306Z", "lastUpdate": "2025-06-30T15:46:01.095401Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "purge_dups", "description": "Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences", "homepage": "https://github.com/dfguan/purge_dups", "biotoolsID": "purge_dups", "biotoolsCURIE": "biotools:purge_dups", "version": [ "v.1.2.6" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0525", "term": "Genome assembly" }, { "uri": "http://edamontology.org/operation_3798", "term": "Read binning" }, { "uri": "http://edamontology.org/operation_3216", "term": "Scaffolding" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "Python", "C" ], "license": "MIT", "collectionID": [ "ONTeater" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/dfguan/purge_dups", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/dfguan/purge_dups/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1101/729962", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Dengfeng Guan", "email": null, "url": "https://www.chatlink.com.cn", "orcidid": "https://orcid.org/0000-0002-6376-3940", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "Pub2Tools", "additionDate": "2019-11-14T18:08:10Z", "lastUpdate": "2025-06-30T15:34:51.626796Z", "editPermission": { "type": "public", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Compleasm", "description": "Compleasm: a faster and more accurate reimplementation of BUSCO.\nIt provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.", "homepage": "https://github.com/huangnengCSU/compleasm", "biotoolsID": "compleasm", "biotoolsCURIE": "biotools:compleasm", "version": [ "v.0.2.5" ], "otherID": [], "relation": [ { "biotoolsID": "busco", "type": "isNewVersionOf" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3180", "term": "Sequence assembly validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2546", "term": "FASTA-like" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2955", "term": "Sequence report" }, "format": [] } ], "note": "Runs compleasm using the BUSCO set corresponding to the lineage given.", "cmd": "compleasm run -l \"$lineage\" -a assembly.fa -o output_prefix" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "ONTeater" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/huangnengCSU/compleasm", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/huangnengCSU/compleasm/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://busco.ezlab.org/list_of_lineages.html", "type": [ "Other" ], "note": "List of accepted lineages (taxonomic groups with curated BUSCO sets)" } ], "download": [], "documentation": [ { "url": "https://github.com/huangnengCSU/compleasm/blob/0.2.6/README.md", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btad595", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "compleasm: a faster and more accurate reimplementation of BUSCO", "abstract": "Motivation: Evaluating the gene completeness is critical to measuring the quality of a genome assembly. An incomplete assembly can lead to errors in gene predictions, annotation, and other downstream analyses. Benchmarking Universal Single-Copy Orthologs (BUSCO) is a widely used tool for assessing the completeness of genome assembly by testing the presence of a set of single-copy orthologs conserved across a wide range of taxa. However, BUSCO is slow particularly for large genome assemblies. It is cumbersome to apply BUSCO to a large number of assemblies. Results: Here, we present compleasm, an efficient tool for assessing the completeness of genome assemblies. Compleasm utilizes the miniprot protein-to-genome aligner and the conserved orthologous genes from BUSCO. It is 14 times faster than BUSCO for human assemblies and reports a more accurate completeness of 99.6% than BUSCO's 95.7%, which is in close agreement with the annotation completeness of 99.5% for T2T-CHM13.", "date": "2023-10-01T00:00:00Z", "citationCount": 95, "authors": [ { "name": "Huang N." }, { "name": "Li H." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Neng Huang", "email": "neng@ds.dfci.harvard.edu", "url": null, "orcidid": "https://orcid.org/0000-0001-7187-0749", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "rlibouban", "additionDate": "2024-03-18T14:51:49.667412Z", "lastUpdate": "2025-06-30T15:30:41.266812Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SILVA rRNA database", "description": "SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukaryota).", "homepage": "https://www.arb-silva.de", "biotoolsID": "silva", "biotoolsCURIE": "biotools:silva", "version": [], "otherID": [ { "value": "RRID:SCR_006423", "type": "rrid", "version": null } ], "relation": [ { "biotoolsID": "silvangs", "type": "usedBy" }, { "biotoolsID": "d3hub", "type": "includedIn" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1097", "term": "Sequence accession (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] }, { "data": { "uri": "http://edamontology.org/data_1868", "term": "Taxon" }, "format": [ { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] }, { "data": { "uri": "http://edamontology.org/data_1046", "term": "Strain name" }, "format": [ { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] }, { "data": { "uri": "http://edamontology.org/data_1088", "term": "Article ID" }, "format": [ { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] }, { "data": { "uri": "http://edamontology.org/data_2909", "term": "Organism name" }, "format": [ { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2955", "term": "Sequence report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] }, { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_3830", "term": "ARB" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] }, { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_3830", "term": "ARB" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] } ], "note": "The search and retrieval functions of the SILVA website can be used to build custom subsets of sequences. In addition to simple searches e.g. for accession numbers, organism names, taxonomic entities, or publication DOI/PubMed IDs, complex queries over several database fields using constraints such as sequence length or quality values are possible. The results can be sorted according to accession numbers, organism names, sequence length, sequence and alignment quality and Pintail values. The search results show accession number, organism name, sequence length, sequence quality values, taxonomic classifications, and links to view the full sequence record on SILVA and on ENA. Sequences found via search and added to download cart can be downloaded as FASTA and ARB files.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2419", "term": "Primer and probe design" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1207", "term": "nucleotide" } ] }, { "data": { "uri": "http://edamontology.org/data_1240", "term": "PCR primers" }, "format": [ { "uri": "http://edamontology.org/format_1207", "term": "nucleotide" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] }, { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] }, { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_3830", "term": "ARB" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] }, { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_3830", "term": "ARB" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] } ], "note": "The SILVA Probe Match and Evaluation Tool detects and displays all occurrences of a given probe or primer sequence in the SILVA datasets. \n\nTestPrime allows you to evaluate the performance of primer pairs by running an in silico PCR on the SILVA databases. From the results of the PCR, TestPrime computes coverages for each taxonomic group in all of the taxonomies offered by SILVA.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" }, { "uri": "http://edamontology.org/operation_0496", "term": "Global alignment" }, { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" }, { "uri": "http://edamontology.org/operation_0547", "term": "Phylogenetic inference (maximum likelihood and Bayesian methods)" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_3830", "term": "ARB" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] }, { "data": { "uri": "http://edamontology.org/data_0867", "term": "Sequence alignment report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0872", "term": "Phylogenetic tree" }, "format": [ { "uri": "http://edamontology.org/format_1910", "term": "newick" } ] }, { "data": { "uri": "http://edamontology.org/data_1872", "term": "Taxonomic classification" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": "The Alignment, Classification and Tree Service (ACT) of SILVA allows to align and optionally classify sequences using the SILVA Incremental Aligner (SINA). From aligned sequences, (optionally) phylogenetic trees can be inferred using FastTree or RAxML.", "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0659", "term": "Functional, regulatory and non-coding RNA" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" }, { "uri": "http://edamontology.org/topic_0637", "term": "Taxonomy" }, { "uri": "http://edamontology.org/topic_3050", "term": "Biodiversity" }, { "uri": "http://edamontology.org/topic_3301", "term": "Microbiology" }, { "uri": "http://edamontology.org/topic_0632", "term": "Probes and primers" } ], "operatingSystem": [], "language": [], "license": "CC-BY-4.0", "collectionID": [ "de.NBI", "de.NBI-biodata", "DSMZ Digital Diversity" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Data" ], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://www.arb-silva.de/browser/", "type": [ "Service" ], "note": "SILVA Taxonomy Browser" }, { "url": "https://www.arb-silva.de/search/", "type": [ "Service" ], "note": "SILVA metadata search" }, { "url": "https://www.arb-silva.de/aligner/", "type": [ "Service" ], "note": "ACT: Alignment, Classification and Tree Service" }, { "url": "https://www.arb-silva.de/search/testprobe/", "type": [ "Service" ], "note": "SILVA Probe Match and Evaluation Tool" }, { "url": "https://www.arb-silva.de/search/testprime/", "type": [ "Service" ], "note": "SILVA Primer Evaluation Tool" }, { "url": "https://treeviewer.arb-silva.de/", "type": [ "Service" ], "note": "Web-based viewer for the SILVA guide trees" } ], "download": [ { "url": "https://www.arb-silva.de/download/archive/", "type": "Downloads page", "note": "SILVA dataset archive", "version": null } ], "documentation": [ { "url": "https://www.arb-silva.de/silva-license-information/", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.arb-silva.de/contact/", "type": [ "Citation instructions" ], "note": null }, { "url": "https://www.arb-silva.de/documentation/", "type": [ "General" ], "note": null }, { "url": "https://www.arb-silva.de/documentation/faqs/", "type": [ "FAQ" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gks1219", "pmid": "23193283", "pmcid": "PMC3531112", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools", "abstract": "SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3194 778 small subunit and 288717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches. © The Author(s) 2012.", "date": "2013-01-01T00:00:00Z", "citationCount": 22633, "authors": [ { "name": "Quast C." }, { "name": "Pruesse E." }, { "name": "Yilmaz P." }, { "name": "Gerken J." }, { "name": "Schweer T." }, { "name": "Yarza P." }, { "name": "Peplies J." }, { "name": "Glockner F.O." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkt1209", "pmid": "24293649", "pmcid": "PMC3965112", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The SILVA and \"all-species Living Tree Project (LTP)\" taxonomic frameworks", "abstract": "SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA genes. This article describes the improvements the SILVA taxonomy has undergone in the last 3 years. Specifically we are focusing on the curation process, the various resources used for curation and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies. Our comparisons not only revealed a reasonable overlap between the taxa names, but also points to significant differences in both names and numbers of taxa between the three resources. © 2013 The Author(s). Published by Oxford University Press.", "date": "2014-01-01T00:00:00Z", "citationCount": 2590, "authors": [ { "name": "Yilmaz P." }, { "name": "Parfrey L.W." }, { "name": "Yarza P." }, { "name": "Gerken J." }, { "name": "Pruesse E." }, { "name": "Quast C." }, { "name": "Schweer T." }, { "name": "Peplies J." }, { "name": "Ludwig W." }, { "name": "Glockner F.O." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkm864", "pmid": "17947321", "pmcid": "PMC2175337", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB", "abstract": "Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction, nucleic acid based detection and quantification of microbial diversity. The ARB software suite with its corresponding rRNA datasets has been accepted by researchers worldwide as a standard tool for large scale rRNA analysis. However, the rapid increase of publicly available rRNA sequence data has recently hampered the maintenance of comprehensive and curated rRNA knowledge databases. A new system, SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains. All sequences are checked for anomalies, carry a rich set of sequence associated contextual information, have multiple taxonomic classifications, and the latest validly described nomenclature. Furthermore, two precompiled sequence datasets compatible with ARB are offered for download on the SILVA website: (i) the reference (Ref) datasets, comprising only high quality, nearly full length sequences suitable for in-depth phylogenetic analysis and probe design and (ii) the comprehensive Parc datasets with all publicly available rRNA sequences longer than 300 nucleotides suitable for biodiversity analyses. The latest publicly available database release 91 (August 2007) hosts 547 521 sequences split into 461 823 small subunit and 85 689 large subunit rRNAs. © 2007 The Author(s).", "date": "2007-12-01T00:00:00Z", "citationCount": 5291, "authors": [ { "name": "Pruesse E." }, { "name": "Quast C." }, { "name": "Knittel K." }, { "name": "Fuchs B.M." }, { "name": "Ludwig W." }, { "name": "Peplies J." }, { "name": "Glockner F.O." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/bioinformatics/bts252", "pmid": "22556368", "pmcid": "PMC3389763", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes", "abstract": "Motivation: In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements.Results: In this study, we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising 38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. © The Author(s) 2012. Published by Oxford University Press.", "date": "2012-07-01T00:00:00Z", "citationCount": 2408, "authors": [ { "name": "Pruesse E." }, { "name": "Peplies J." }, { "name": "Glockner F.O." } ], "journal": "Bioinformatics" } }, { "doi": "10.1016/j.jbiotec.2017.06.1198", "pmid": "28648396", "pmcid": null, "type": [ "Review" ], "version": null, "note": null, "metadata": { "title": "25 years of serving the community with ribosomal RNA gene reference databases and tools", "abstract": "SILVA (lat. forest) is a comprehensive web resource, providing services around up to date, high-quality datasets of aligned ribosomal RNA gene (rDNA) sequences from the Bacteria, Archaea, and Eukaryota domains. SILVA dates back to the year 1991 when Dr. Wolfgang Ludwig from the Technical University Munich started the integrated software workbench ARB (lat. tree) to support high-quality phylogenetic inference and taxonomy based on the SSU and LSU rDNA marker genes. At that time, the ARB project maintained both, the sequence reference datasets and the software package for data analysis. In 2005, with the massive increase of DNA sequence data, the maintenance of the software system ARB and the corresponding rRNA databases SILVA was split between Munich and the Microbial Genomics and Bioinformatics Research Group in Bremen. ARB has been continuously developed to include new features and improve the usability of the workbench. Thousands of users worldwide appreciate the seamless integration of common analysis tools under a central graphical user interface, in combination with its versatility. The first SILVA release was deployed in February 2007 based on the EMBL-EBI/ENA release 89. Since then, full SILVA releases offering the database content in various flavours are published at least annually, complemented by intermediate web-releases where only the SILVA web dataset is updated. SILVA is the only rDNA database project worldwide where special emphasis is given to the consistent naming of clades of uncultivated (environmental) sequences, where no validly described cultivated representatives are available. Also exclusive for SILVA is the maintenance of both comprehensive aligned 16S/18S rDNA and 23S/28S rDNA sequence datasets. Furthermore, the SILVA alignments and trees were designed to include Eukaryota, another unique feature among rDNA databases. With the termination of the European Ribosomal RNA Database Project in 2007, the SILVA database has become the authoritative rDNA database project for Europe. The application spectrum of ARB and SILVA ranges from biodiversity analysis, medical diagnostics, to biotechnology and quality control for academia and industry.", "date": "2017-11-10T00:00:00Z", "citationCount": 635, "authors": [ { "name": "Glockner F.O." }, { "name": "Yilmaz P." }, { "name": "Quast C." }, { "name": "Gerken J." }, { "name": "Beccati A." }, { "name": "Ciuprina A." }, { "name": "Bruns G." }, { "name": "Yarza P." }, { "name": "Peplies J." }, { "name": "Westram R." }, { "name": "Ludwig W." } ], "journal": "Journal of Biotechnology" } }, { "doi": "10.1186/s12859-017-1841-3", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "SILVA tree viewer: Interactive web browsing of the SILVA phylogenetic guide trees", "abstract": "Background: Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the taxonomic framework. Results: The SILVA Tree Viewer is a web application designed for visualizing large phylogenetic trees without requiring the download of any software tool or data files. The SILVA Tree Viewer is based on Web Geographic Information Systems (Web-GIS) technology with a PostgreSQL backend. It enables zoom and pan functionalities similar to Google Maps. The SILVA Tree Viewer enables access to two phylogenetic (guide) trees provided by the SILVA database: the SSU Ref NR99 inferred from high-quality, full-length small subunit sequences, clustered at 99% sequence identity and the LSU Ref inferred from high-quality, full-length large subunit sequences. Conclusions: The Tree Viewer provides tree navigation, search and browse tools as well as an interactive feedback system to collect any kinds of requests ranging from taxonomy to data curation and improving the tool itself.", "date": "2017-09-30T00:00:00Z", "citationCount": 29, "authors": [ { "name": "Beccati A." }, { "name": "Gerken J." }, { "name": "Quast C." }, { "name": "Yilmaz P." }, { "name": "Glockner F.O." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures", "email": "hub@dsmz.de", "url": "https://www.dsmz.de", "orcidid": null, "gridid": "grid.420081.f", "rorid": "02tyer376", "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "SILVA Team", "email": "contact@arb-silva.de", "url": "https://www.arb-silva.de/contact/team/", "orcidid": null, "gridid": "grid.507782.f", "rorid": "027z9pz32", "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "silva", "additionDate": "2016-09-30T15:59:05Z", "lastUpdate": "2025-06-30T13:26:42.882897Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "FAIR_EVA", "description": "FAIR EVA: Evaluator, Validator & Advisor has been developed to check the FAIRness level of digital objects from different repositories or data portals. It requires the object identifier (preferably persistent and unique identifier) and the repository to check. It also provides a generic and agnostic way to check digital objects.", "homepage": "https://github.com/IFCA-Advanced-Computing/FAIR_eva", "biotoolsID": "fair_eva_4_eucaim", "biotoolsCURIE": "biotools:fair_eva_4_eucaim", "version": [ "EUCAIM_plugin_1" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Web service", "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_4012", "term": "FAIR data" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://github.com/IFCA-Advanced-Computing/FAIR_eva/blob/main/docs/index.md", "type": [ "Quick start guide" ], "note": "Documentation for the main package, EUCAIM plugin specific documentation not included." } ], "publication": [ { "doi": "10.1038/s41597-023-02652-8", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "FAIR EVA: Bringing institutional multidisciplinary repositories into the FAIR picture", "abstract": "The FAIR Principles are a set of good practices to improve the reproducibility and quality of data in an Open Science context. Different sets of indicators have been proposed to evaluate the FAIRness of digital objects, including datasets that are usually stored in repositories or data portals. However, indicators like those proposed by the Research Data Alliance are provided from a high-level perspective that can be interpreted and they are not always realistic to particular environments like multidisciplinary repositories. This paper describes FAIR EVA, a new tool developed within the European Open Science Cloud context that is oriented to particular data management systems like open repositories, which can be customized to a specific case in a scalable and automatic environment. It aims to be adaptive enough to work for different environments, repository software and disciplines, taking into account the flexibility of the FAIR Principles. As an example, we present DIGITAL.CSIC repository as the first target of the tool, gathering the particular needs of a multidisciplinary institution as well as its institutional repository.", "date": "2023-12-01T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Aguilar Gomez F." }, { "name": "Bernal I." } ], "journal": "Scientific Data" } } ], "credit": [ { "name": "European Union’s Horizon 2020 research and innovation programme", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": "This software started to be developed within IFCA-Advanced-Computing receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 857647." } ], "owner": "davrodgon", "additionDate": "2025-06-30T08:52:48.500476Z", "lastUpdate": "2025-06-30T09:00:26.819772Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, 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"http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1101/2024.02.28.582465", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1101/2024.02.14.580341", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "arojas", "additionDate": "2024-07-12T13:51:31.192159Z", "lastUpdate": "2025-06-28T15:45:24.390300Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DALIA", "description": "DALIA promotes the learning and teaching of Data Literacy through the curated supply of open teaching and learning content, empowering everyone to collect, analyze, critically evaluate, and use data in a FAIR way.", "homepage": "https://search.dalia.education", "biotoolsID": "dalia", "biotoolsCURIE": "biotools:dalia", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application", "Database portal", "SPARQL endpoint", "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_4012", "term": "FAIR data" }, { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://git.rwth-aachen.de/dalia", "type": [ "Repository" ], "note": null }, { "url": "https://nfdi.social/@dalia", "type": [ "Social media" ], "note": null }, { "url": "https://bsky.app/profile/daliaeducation.bsky.social", "type": [ "Social media" ], "note": null }, { "url": "https://dalia.education/en/newsletter", "type": [ "Other" ], "note": "Newsletter" } ], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Sonja Herres-Pawlis", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-4354-4353", "gridid": null, "rorid": "04xfq0f34", "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "cthoyt", "additionDate": "2025-06-26T12:43:43.738614Z", "lastUpdate": "2025-06-26T13:20:18.702036Z", "editPermission": { "type": "group", "authors": [ "jortmeyer" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "The MINERVA Platform", "description": "The MINERVA (Molecular Interaction NEtwoRk VisuAlization) platform is a standalone webserver for visualization, exploration and management of molecular networks encoded in SBGN-compliant format, including files produced using CellDesigner or SBGN editors. Visualization of uploaded networks generated by the platform is accessible via a web browser to all viewers with the weblink to the resource.\n\nThe MINERVA Platform is a webservice using the Java Server Faces 2 technology. The server side, including data parsing, integration, annotation and verification, is implemented in Java. The platform uses the Postgres SQL database for data storage and the Hibernate framework as a middle layer between web server and database. The user web-interface is generated using React.js. The displayed content is visualized by OpenLayers API, dedicated JavaScript and CSS.", "homepage": "https://minerva.uni.lu", "biotoolsID": "MINERVA_Platform", "biotoolsCURIE": "biotools:MINERVA_Platform", "version": [ "13.1.3", "13.2.0", "14.0.13", "15.0.3", "16.4.0", "17.1.3", "18.1.1" ], "otherID": [], "relation": [ { "biotoolsID": "pathvisio", "type": "uses" }, { "biotoolsID": "sbgn", "type": "uses" }, { "biotoolsID": "libsbml", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3926", "term": "Pathway visualisation" } ], "input": [], "output": [], "note": "Visualise systems biology diagrams online, on a standalone web server", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0571", "term": "Expression data visualisation" } ], "input": [], "output": [], "note": "Visualise omics data from multiple datasets on top of the diagrams", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [], "output": [], "note": "Convert between main systems biology layout formats: CellDeslgners SBML, SBML layout+render, SBGN-ML, GPML", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" } ], "input": [], "output": [], "note": "Use MINERVA API to access systems biology formats for modelling", "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3391", "term": "Omics" }, { "uri": "http://edamontology.org/topic_3342", "term": "Translational medicine" }, { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" } ], "operatingSystem": [], "language": [], "license": "AGPL-3.0", "collectionID": [ "ELIXIR-LU", "LCSB" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Luxembourg" ], "elixirCommunity": [], "link": [ { "url": "https://gitlab.lcsb.uni.lu/minerva/core/", "type": [ "Repository" ], "note": "GiLab repository for core functionalities (data and format handling, service stability, API access)" }, { "url": "https://gitlab.lcsb.uni.lu/minerva/core/-/issues", "type": [ "Issue tracker" ], "note": "Issue tracker for core functionalities (data and format handling, service stability, API access)" }, { "url": "https://gitlab.lcsb.uni.lu/minerva/frontend", "type": [ "Repository" ], "note": "GiLab repository for frontend functionalities" }, { "url": "https://gitlab.lcsb.uni.lu/minerva/frontend/-/issues", "type": [ "Issue tracker" ], "note": "Issue tracker for frontend functionalities" } ], "download": [ { "url": "https://minerva.pages.uni.lu/doc/install/", "type": "Other", "note": "Installation instructions, including debian package, virtual machine images and docker containers.", "version": "13.1.3 - 18.1.1" } ], "documentation": [ { "url": "https://minerva.uni.lu", "type": [ "Quick start guide", "Release notes", "User manual", "API documentation", "Citation instructions", "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.1038/npjsba.2016.20", "pmid": "28725475", "pmcid": "PMC5516855", "type": [ "Primary" ], "version": "10.0", "note": null, "metadata": { "title": "MINERVA—A platform for visualization and curation of molecular interaction networks", "abstract": "Our growing knowledge about various molecular mechanisms is becoming increasingly more structured and accessible. Different repositories of molecular interactions and available literature enable construction of focused and high-quality molecular interaction networks. Novel tools for curation and exploration of such networks are needed, in order to foster the development of a systems biology environment. In particular, solutions for visualization, annotation and data cross-linking will facilitate usage of network-encoded knowledge in biomedical research. To this end we developed the MINERVA (Molecular Interaction NEtwoRks VisuAlization) platform, a standalone webservice supporting curation, annotation and visualization of molecular interaction networks in Systems Biology Graphical Notation (SBGN)-compliant format. MINERVA provides automated content annotation and verification for improved quality control. The end users can explore and interact with hosted networks, and provide direct feedback to content curators. MINERVA enables mapping drug targets or overlaying experimental data on the visualized networks. Extensive export functions enable downloading areas of the visualized networks as SBGN-compliant models for efficient reuse of hosted networks. The software is available under Affero GPL 3.0 as a Virtual Machine snapshot, Debian package and Docker instance at http://r3lab.uni.lu/web/minerva-website/. We believe that MINERVA is an important contribution to systems biology community, as its architecture enables set-up of locally or globally accessible SBGN-oriented repositories of molecular interaction networks. Its functionalities allow overlay of multiple information layers, facilitating exploration of content and interpretation of data. Moreover, annotation and verification workflows of MINERVA improve the efficiency of curation of networks, allowing life-science researchers to better engage in development and use of biomedical knowledge repositories.", "date": "2016-01-01T00:00:00Z", "citationCount": 65, "authors": [ { "name": "Gawron P." }, { "name": "Ostaszewski M." }, { "name": "Satagopam V." }, { "name": "Gebel S." }, { "name": "Mazein A." }, { "name": "Kuzma M." }, { "name": "Zorzan S." }, { "name": "McGee F." }, { "name": "Otjacques B." }, { "name": "Balling R." }, { "name": "Schneider R." } ], "journal": "npj Systems Biology and Applications" } }, { "doi": "10.1093/bioinformatics/btz286", "pmid": "31074494", "pmcid": "PMC6821317", "type": [ "Primary" ], "version": "12.2.3", "note": null, "metadata": { "title": "MINERVA API and plugins: Opening molecular network analysis and visualization to the community", "abstract": "Summary: The complexity of molecular networks makes them difficult to navigate and interpret, creating a need for specialized software. MINERVA is a web platform for visualization, exploration and management of molecular networks. Here, we introduce an extension to MINERVA architecture that greatly facilitates the access and use of the stored molecular network data. It allows to incorporate such data in analytical pipelines via a programmatic access interface, and to extend the platform's visual exploration and analytics functionality via plugin architecture. This is possible for any molecular network hosted by the MINERVA platform encoded in well-recognized systems biology formats. To showcase the possibilities of the plugin architecture, we have developed several plugins extending the MINERVA core functionalities. In the article, we demonstrate the plugins for interactive tree traversal of molecular networks, for enrichment analysis and for mapping and visualization of known disease variants or known adverse drug reactions to molecules in the network. Availability and implementation: Plugins developed and maintained by the MINERVA team are available under the AGPL v3 license at https://git-r3lab.uni.lu/minerva/plugins/. The MINERVA API and plugin documentation is available at https://minerva-web.lcsb.uni.lu.", "date": "2019-11-01T00:00:00Z", "citationCount": 25, "authors": [ { "name": "Hoksza D." }, { "name": "Gawron P." }, { "name": "Ostaszewski M." }, { "name": "Smula E." }, { "name": "Schneider R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/bib/bbz067", "pmid": "31273380", "pmcid": "PMC7373180", "type": [ "Primary" ], "version": "13.1.1", "note": null, "metadata": { "title": "Closing the gap between formats for storing layout information in systems biology", "abstract": "The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no software tools or software libraries supporting all of them. This complicates the management of molecular network layouts and hinders their reuse and extension. In this paper, we present a high-level overview of the layout formats in systems biology, focusing on their commonalities and differences, review their support in existing software tools, libraries and repositories and finally introduce a new conversion module within the MINERVA platform. The module is available via a REST API and offers, besides the ability to convert between layout-aware systems biology formats, the possibility to export layouts into several graphical formats. The module enables conversion of very large networks with thousands of elements, such as disease maps or metabolic reconstructions, rendering it widely applicable in systems biology.", "date": "2019-07-10T00:00:00Z", "citationCount": 17, "authors": [ { "name": "Hoksza D." }, { "name": "Gawron P." }, { "name": "Ostaszewski M." }, { "name": "Hasenauer J." }, { "name": "Schneider R." } ], "journal": "Briefings in Bioinformatics" } }, { "doi": "10.1089/big.2015.0057", "pmid": "27441714", "pmcid": "PMC4932659", "type": [ "Usage" ], "version": "10.0", "note": null, "metadata": { "title": "Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases", "abstract": "Translational medicine is a domain turning results of basic life science research into new tools and methods in a clinical environment, for example, as new diagnostics or therapies. Nowadays, the process of translation is supported by large amounts of heterogeneous data ranging from medical data to a whole range of -omics data. It is not only a great opportunity but also a great challenge, as translational medicine big data is difficult to integrate and analyze, and requires the involvement of biomedical experts for the data processing. We show here that visualization and interoperable workflows, combining multiple complex steps, can address at least parts of the challenge. In this article, we present an integrated workflow for exploring, analysis, and interpretation of translational medicine data in the context of human health. Three Web services - tranSMART, a Galaxy Server, and a MINERVA platform - are combined into one big data pipeline. Native visualization capabilities enable the biomedical experts to get a comprehensive overview and control over separate steps of the workflow. The capabilities of tranSMART enable a flexible filtering of multidimensional integrated data sets to create subsets suitable for downstream processing. A Galaxy Server offers visually aided construction of analytical pipelines, with the use of existing or custom components. A MINERVA platform supports the exploration of health and disease-related mechanisms in a contextualized analytical visualization system. We demonstrate the utility of our workflow by illustrating its subsequent steps using an existing data set, for which we propose a filtering scheme, an analytical pipeline, and a corresponding visualization of analytical results. The workflow is available as a sandbox environment, where readers can work with the described setup themselves. Overall, our work shows how visualization and interfacing of big data processing services facilitate exploration, analysis, and interpretation of translational medicine data.", "date": "2016-06-01T00:00:00Z", "citationCount": 39, "authors": [ { "name": "Satagopam V." }, { "name": "Gu W." }, { "name": "Eifes S." }, { "name": "Gawron P." }, { "name": "Ostaszewski M." }, { "name": "Gebel S." }, { "name": "Barbosa-Silva A." }, { "name": "Balling R." }, { "name": "Schneider R." } ], "journal": "Big Data" } }, { "doi": "10.1016/j.envpol.2019.04.005", "pmid": "30991279", "pmcid": null, "type": [], "version": "13.1.1", "note": null, "metadata": { "title": "Genes associated with Parkinson's disease respond to increasing polychlorinated biphenyl levels in the blood of healthy females", "abstract": "Polychlorinated biphenyls (PCBs) are a class of widespread environmental pollutants, commonly found in human blood, that have been suggested to be linked to the occurrence of sporadic Parkinson's disease (PD). It has been reported that some non-coplanar PCBs accumulate in the brains of female PD patients. To improve our understanding of the association between PCB exposure and PD risk we have applied whole transcriptome gene expression analysis in blood cells from 594 PCB-exposed subjects (369 female, 225 male). Interestingly, we observe that in females, blood levels of non-coplanar PCBs appear to be associated with expression levels of PD-specific genes. However, no such association was detected in males. Among the 131 PD-specific genes affected, 39 have been shown to display similar changes in expression levels in the substantia nigra of deceased PD patients. Especially among the down-regulated genes, transcripts of genes involved in neurotransmitter vesicle-related functions were predominant. Capsule: Plasma PCB levels are associated with gene expression changes in females only, resulting in brain-related genes changing in blood cells of healthy individuals exposed to PCBs.", "date": "2019-07-01T00:00:00Z", "citationCount": 5, "authors": [ { "name": "Bohler S." }, { "name": "Krauskopf J." }, { "name": "Espin-Perez A." }, { "name": "Gebel S." }, { "name": "Palli D." }, { "name": "Rantakokko P." }, { "name": "Kiviranta H." }, { "name": "Kyrtopoulos S.A." }, { "name": "Balling R." }, { "name": "Kleinjans J." } ], "journal": "Environmental Pollution" } } ], "credit": [], "owner": "mjostaszewski", "additionDate": "2019-08-26T14:34:55Z", "lastUpdate": "2025-06-26T13:15:59.673112Z", "editPermission": { "type": "group", "authors": [ "sascha.herzinger" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FANTASIAV2", "description": "FANTASIA (Functional ANnoTAtion based on embedding space SImilArity) is a pipeline for protein annotating via GO term transference using the embedding space. FANTASIA’s latest developments include additional protein language models and provide enhanced functionalities.", "homepage": "https://github.com/CBBIO/FANTASIA", "biotoolsID": "fantasiav2", "biotoolsCURIE": "biotools:fantasiav2", "version": [ "2.8.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3672", "term": "Gene functional annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3945", "term": "Molecular evolution" }, { "uri": "http://edamontology.org/topic_0218", "term": "Natural language processing" }, { "uri": "http://edamontology.org/topic_0085", "term": "Functional genomics" }, { "uri": "http://edamontology.org/topic_4010", "term": "Open science" } ], "operatingSystem": [ "Linux" ], "language": [ "Python", "SQL" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Spain" ], "elixirCommunity": [ "3D-BioInfo", "Proteomics" ], "link": [ { "url": "https://github.com/CBBIO/FANTASIA", "type": [ "Repository" ], "note": "Main repository contains documentation from latest version" }, { "url": "https://github.com/MetazoaPhylogenomicsLab/FANTASIA", "type": [ "Repository" ], "note": "Main repository contains documentation from linitial version based on Bioembeddings implementation." }, { "url": "https://www.earthbiogenome.org/report-on-annotation-recommended-tools", "type": [ "Software catalogue" ], "note": "Recommended tool for the Earth Biogenome Project" } ], "download": [], "documentation": [ { "url": "https://fantasia.readthedocs.io/en/latest/", "type": [ "General" ], "note": "Full documetnation with user cases, benchmarking, and cluster implementations" } ], "publication": [ { "doi": "10.1093/nargab/lqae078", "pmid": null, "pmcid": null, "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Decoding functional proteome information in model organisms using protein language models", "abstract": "Protein language models have been tested and proved to be reliable when used on curated datasets but have not yet been applied to full proteomes. Accordingly, we tested how two different machine learning-based methods performed when decoding functional information from the proteomes of selected model organisms. We found that protein language models are more precise and informative than deep learning methods for all the species tested and across the three gene ontologies studied, and that they better recover functional information from transcriptomic experiments. The results obtained indicate that these language models are likely to be suitable for large-scale annotation and downstream analyses, and we recommend a guide for their use.", "date": "2024-09-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Barrios-Nunez I." }, { "name": "Martinez-Redondo G.I." }, { "name": "Medina-Burgos P." }, { "name": "Cases I." }, { "name": "Fernandez R." }, { "name": "Rojas A.M." } ], "journal": "NAR Genomics and Bioinformatics" } }, { "doi": "10.1101/2024.02.28.582465", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Francisco Miguel Pérez Canales", "email": "fmpercan@upo.es", "url": "http://www.bioinfocb.es/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer", "Support", "Provider" ], "note": "Programmer" }, { "name": "Ana M Rojas Mendoza", "email": "a.rojas.m@csic.es", "url": "http://www.bioinfocb.es/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Contributor", "Documentor", "Support" ], "note": "Scientific concept and functionalities" }, { "name": "Rosa Fernandez", "email": "rosa.fernandez@ibe.upf-csic.es", "url": "https://www.metazomics.com/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Documentor" ], "note": "Scientific concept and functionalities" }, { "name": "Francisco J. Ruiz Mota", "email": "fraruimot@alum.us.es", "url": "http://www.bioinfocb.es/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": "Junior developer" }, { "name": "Gemma Martinez Redondo", "email": "gemma.martinez@ibe.upf-csic.es", "url": "https://www.metazomics.com/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Developer" ], "note": "Contributed as developer of the first version of FANTASIA V1" } ], "owner": "arojas", "additionDate": "2025-06-25T13:31:29.384393Z", "lastUpdate": "2025-06-25T14:34:50.629045Z", "editPermission": { "type": "group", "authors": [ "frapercan" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "DeepSig", "description": "Prediction of secretory signal peptides in protein sequences", "homepage": "https://busca.biocomp.unibo.it/deepsig/", "biotoolsID": "deepsig", "biotoolsCURIE": "biotools:deepsig", "version": [ "1.2.5" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0418", "term": "Protein signal peptide detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2974", "term": "Protein sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0896", "term": "Protein report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0123", "term": "Protein properties" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python", "C++" ], "license": "GPL-3.0", "collectionID": [ "Bologna Biocomputing Group" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/BolognaBiocomp/deepsig", "type": "Source code", "note": null, "version": "1.2.5" }, { "url": "https://hub.docker.com/r/bolognabiocomp/deepsig", "type": "Container file", "note": null, "version": "1.2.5" } ], "documentation": [ { "url": "https://github.com/BolognaBiocomp/deepsig", "type": [ "Command-line options" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btx818", "pmid": "29280997", "pmcid": "PMC5946842", "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "DeepSig: Deep learning improves signal peptide detection in proteins", "abstract": "Motivation The identification of signal peptides in protein sequences is an important step toward protein localization and function characterization. Results Here, we present DeepSig, an improved approach for signal peptide detection and cleavage-site prediction based on deep learning methods. Comparative benchmarks performed on an updated independent dataset of proteins show that DeepSig is the current best performing method, scoring better than other available state-of-the-art approaches on both signal peptide detection and precise cleavage-site identification. Availability and implementation DeepSig is available as both standalone program and web server at https://deepsig.biocomp.unibo.it. All datasets used in this study can be obtained from the same website.", "date": "2018-05-15T00:00:00Z", "citationCount": 96, "authors": [ { "name": "Savojardo C." }, { "name": "Martelli P.L." }, { "name": "Fariselli P." }, { "name": "Casadio R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": "http://biocomp.unibo.it", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Castrense Savojardo", "email": "castrense.savojardo2@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-7359-0633", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact" ], "note": null }, { "name": "Pier Luigi Martelli", "email": "pierluigi.martelli@unibo.it", "url": "http://biocomp.unibo.it", "orcidid": "https://orcid.org/0000-0002-0274-5669", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2018-05-28T14:50:09Z", "lastUpdate": "2025-06-19T11:55:09.017105Z", "editPermission": { "type": "group", "authors": [ "savo", "ELIXIR-ITA-BOLOGNA" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "QIIME 2", "description": "QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics.", "homepage": "https://qiime2.org", "biotoolsID": "qiime2", "biotoolsCURIE": "biotools:qiime2", "version": [ "2.0" ], "otherID": [], "relation": [ { "biotoolsID": "qiime", "type": "isNewVersionOf" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3933", "term": "Demultiplexing" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Suite", "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" }, { "uri": "http://edamontology.org/topic_3941", "term": "Metatranscriptomics" }, { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "BSD-3-Clause", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [ "Galaxy" ], "link": [ { "url": "https://github.com/qiime2", "type": [ "Repository" ], "note": null }, { "url": "https://library.qiime2.org", "type": [ "Software catalogue" ], "note": null }, { "url": "https://forum.qiime2.org", "type": [ "Discussion forum" ], "note": null }, { "url": "https://view.qiime2.org", "type": [ "Other" ], "note": "Site for viewing and interacting with QIIME 2 results." } ], "download": [], "documentation": [ { "url": "https://amplicon-docs.qiime2.org", "type": [ "General" ], "note": "User documentation for amplicon analysis, oriented to new users." }, { "url": "https://moshpit.qiime2.org", "type": [ "Installation instructions" ], "note": "User documentation for metagenome analysis, oriented to new users." }, { "url": "https://use.qiime2.org", "type": [ "User manual" ], "note": "User documentation, oriented toward power users." }, { "url": "https://develop.qiime2.org", "type": [ "API documentation" ], "note": "Developer documentation, including a plugin development tutorial." }, { "url": "https://library.qiime2.org/books", "type": [ "Other" ], "note": "The QIIME 2 Library Stacks: a resource for discovering relevant documentation." } ], "publication": [ { "doi": "10.1038/s41587-019-0209-9", "pmid": "31341288", "pmcid": "PMC7015180", "type": [ "Primary" ], "version": "2.0", "note": null, "metadata": { "title": "Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2", "abstract": "", "date": "2019-08-01T00:00:00Z", "citationCount": 14289, "authors": [ { "name": "Bolyen E." }, { "name": "Rideout J.R." }, { "name": "Dillon M.R." }, { "name": "Bokulich N.A." }, { "name": "Abnet C.C." }, { "name": "Al-Ghalith G.A." }, { "name": "Alexander H." }, { "name": "Alm E.J." }, { "name": "Arumugam M." }, { "name": "Asnicar F." }, { "name": "Bai Y." }, { "name": "Bisanz J.E." }, { "name": "Bittinger K." }, { "name": "Brejnrod A." }, { "name": "Brislawn C.J." }, { "name": "Brown C.T." }, { "name": "Callahan B.J." }, { "name": "Caraballo-Rodriguez A.M." }, { "name": "Chase J." }, { "name": "Cope E.K." }, { "name": "Da Silva R." }, { "name": "Diener C." }, { "name": "Dorrestein P.C." }, { "name": "Douglas G.M." }, { "name": "Durall D.M." }, { "name": "Duvallet C." }, { "name": "Edwardson C.F." }, { "name": "Ernst M." }, { "name": "Estaki M." }, { "name": "Fouquier J." }, { "name": "Gauglitz J.M." }, { "name": "Gibbons S.M." }, { "name": "Gibson D.L." }, { "name": "Gonzalez A." }, { "name": "Gorlick K." }, { "name": "Guo J." }, { "name": "Hillmann B." }, { "name": "Holmes S." }, { "name": "Holste H." }, { "name": "Huttenhower C." }, { "name": "Huttley G.A." }, { "name": "Janssen S." }, { "name": "Jarmusch A.K." }, { "name": "Jiang L." }, { "name": "Kaehler B.D." }, { "name": "Kang K.B." }, { "name": "Keefe C.R." }, { "name": "Keim P." }, { "name": "Kelley S.T." }, { "name": "Knights D." }, { "name": "Koester I." }, { "name": "Kosciolek T." }, { "name": "Kreps J." }, { "name": "Langille M.G.I." }, { "name": "Lee J." }, { "name": "Ley R." }, { "name": "Liu Y.-X." }, { "name": "Loftfield E." }, { "name": "Lozupone C." }, { "name": "Maher M." }, { "name": "Marotz C." }, { "name": "Martin B.D." }, { "name": "McDonald D." }, { "name": "McIver L.J." }, { "name": "Melnik A.V." }, { "name": "Metcalf J.L." }, { "name": "Morgan S.C." }, { "name": "Morton J.T." }, { "name": "Naimey A.T." }, { "name": "Navas-Molina J.A." }, { "name": "Nothias L.F." }, { "name": "Orchanian S.B." }, { "name": "Pearson T." }, { "name": "Peoples S.L." }, { "name": "Petras D." }, { "name": "Preuss M.L." }, { "name": "Pruesse E." }, { "name": "Rasmussen L.B." }, { "name": "Rivers A." }, { "name": "Robeson M.S." }, { "name": "Rosenthal P." }, { "name": "Segata N." }, { "name": "Shaffer M." }, { "name": "Shiffer A." }, { "name": "Sinha R." }, { "name": "Song S.J." }, { "name": "Spear J.R." }, { "name": "Swafford A.D." }, { "name": "Thompson L.R." }, { "name": "Torres P.J." }, { "name": "Trinh P." }, { "name": "Tripathi A." }, { "name": "Turnbaugh P.J." }, { "name": "Ul-Hasan S." }, { "name": "van der Hooft J.J.J." }, { "name": "Vargas F." }, { "name": "Vazquez-Baeza Y." }, { "name": "Vogtmann E." }, { "name": "von Hippel M." }, { "name": "Walters W." }, { "name": "Wan Y." }, { "name": "Wang M." }, { "name": "Warren J." }, { "name": "Weber K.C." }, { "name": "Williamson C.H.D." }, { "name": "Willis A.D." }, { "name": "Xu Z.Z." }, { "name": "Zaneveld J.R." }, { "name": "Zhang Y." }, { "name": "Zhu Q." }, { "name": "Knight R." }, { "name": "Caporaso J.G." } ], "journal": "Nature Biotechnology" } } ], "credit": [ { "name": "Greg Caporaso", "email": "greg.caporaso@nau.edu", "url": "https://cap-lab.bio", "orcidid": "https://orcid.org/0000-0002-8865-1670", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null } ], "owner": "gregcaporaso", "additionDate": "2021-05-27T09:02:10Z", "lastUpdate": "2025-06-18T21:00:46.185472Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MetaSBT", "description": "MetaSBT is a scalable framework designed to automatically index microbial genomes and accurately characterize metagenome-assembled genomes using Sequence Bloom Trees.", "homepage": "https://github.com/cumbof/MetaSBT", "biotoolsID": "metasbt", "biotoolsCURIE": "biotools:metasbt", "version": [ "0.1.4.post1" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/cumbof/MetaSBT", "type": [ "Repository" ], "note": "Framework Repository" }, { "url": "https://github.com/cumbof/MetaSBT-DBs", "type": [ "Repository" ], "note": "Repository with Public MetaSBT Databases" } ], "download": [ { "url": "https://pypi.io/packages/source/m/metasbt/metasbt-0.1.4.post1.tar.gz", "type": "Software package", "note": null, "version": "0.1.4" } ], "documentation": [ { "url": "https://github.com/cumbof/MetaSBT/wiki", "type": [ "General" ], "note": "Official MetaSBT Wiki" } ], "publication": [], "credit": [ { "name": "Fabio Cumbo", "email": "fabio.cumbo@gmail.com", "url": "https://cumbof.github.io", "orcidid": "https://orcid.org/0000-0003-2920-5838", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Developer", "Maintainer", "Support" ], "note": null } ], "owner": "fabiocumbo", "additionDate": "2025-06-17T20:53:54.551980Z", "lastUpdate": "2025-06-18T17:12:50.842659Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "kraken2", "description": "Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.\nAny assumption that Kraken’s raw read assignments can be directly translated into species or strain-level abundance estimates is flawed. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN), estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree. (Lu, Jennifer et al. “Bracken: estimating species abundance in metagenomics data.”)", "homepage": "https://ccb.jhu.edu/software/kraken2/", "biotoolsID": "kraken2", "biotoolsCURIE": "biotools:kraken2", "version": [ "2.0.8-beta" ], "otherID": [], "relation": [ { "biotoolsID": "kraken", "type": "isNewVersionOf" }, { "biotoolsID": "bracken", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": "`kraken2 --db <kraken2_database> <input.fastq>`" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0637", "term": "Taxonomy" }, { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" }, { "uri": "http://edamontology.org/topic_3301", "term": "Microbiology" } ], "operatingSystem": [], "language": [ "C++", "Perl" ], "license": "MIT", "collectionID": [ "ONTeater" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/DerrickWood/kraken2", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/DerrickWood/kraken2/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/DerrickWood/kraken2/archive/v2.0.8-beta.tar.gz", "type": "Source code", "note": null, "version": "2.0.8-beta" } ], "documentation": [ { "url": "https://github.com/DerrickWood/kraken2/wiki/Manual", "type": [ "User manual" ], "note": null }, { "url": "https://benlangmead.github.io/aws-indexes/k2", "type": [ "User manual" ], "note": "Links to multiple Kraken 2 and bracken databases and indexes" } ], "publication": [ { "doi": "10.1101/762302", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Derrick E. Wood", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0002-7429-1854", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Jennifer Lu", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0001-9167-2002", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Ben Langmead", "email": "langmea@cs.jhu.edu", "url": null, "orcidid": "http://orcid.org/0000-0003-2437-1976", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "anand-anshu", "additionDate": "2019-09-13T12:51:16Z", "lastUpdate": "2025-06-18T12:24:26.657325Z", "editPermission": { "type": "group", "authors": [ "vashokan", "Keiler_Collier" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "NextDenovo", "description": "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a \"correct-then-assemble\" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages.", "homepage": "https://github.com/Nextomics/NextDenovo", "biotoolsID": "nextdenovo", "biotoolsCURIE": "biotools:nextdenovo", "version": [ "v.2.5.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0524", "term": "De-novo assembly" }, { "uri": "http://edamontology.org/operation_0525", "term": "Genome assembly" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0925", "term": "Sequence assembly" }, "format": [ { "uri": "http://edamontology.org/format_2561", "term": "Sequence assembly format (text)" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" } ], "operatingSystem": [], "language": [ "Python", "C" ], "license": "GPL-3.0", "collectionID": [ "ONTeater" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/Nextomics/NextDenovo/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/Nextomics/NextDenovo/releases/tag/2.5.2", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://nextdenovo.readthedocs.io/en/latest/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1101/2023.03.09.531669.", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Nextomics", "email": "support@nextomics.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Kigaard", "additionDate": "2021-05-26T21:13:32Z", "lastUpdate": "2025-06-18T12:20:23.607241Z", "editPermission": { "type": "group", "authors": [ "jw", "ELIXIR-CZ", "Keiler_Collier" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "quickmerge", "description": "Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.", "homepage": "https://github.com/mahulchak/quickmerge", "biotoolsID": "quickmerge", "biotoolsCURIE": "biotools:quickmerge", "version": [ "v.0.3" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0525", "term": "Genome assembly" }, { "uri": "http://edamontology.org/operation_3216", "term": "Scaffolding" }, { "uri": "http://edamontology.org/operation_0524", "term": "De-novo assembly" }, { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": "Runs whole merge process on an input assembly.\nAssembly 2 will be used to fill gaps in assembly 1.", "cmd": "merge_wrapper.py -pre output_prefix assembly_1.fa assembly_2.fa" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3175", "term": "Structural variation" }, { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_3673", "term": "Whole genome sequencing" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "C++", "C" ], "license": "GPL-3.0", "collectionID": [ "ONTeater" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/mahulchak/quickmerge/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://github.com/mahulchak/quickmerge", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1534/g3.118.200162", "pmid": "30018084", "pmcid": "PMC6169397", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Rapid low-cost assembly of the drosophila melanogaster reference genome using low-coverage, long-read sequencing", "abstract": "Accurate and comprehensive characterization of genetic variation is essential for deciphering the genetic basis of diseases and other phenotypes. A vast amount of genetic variation stems from largescale sequence changes arising from the duplication, deletion, inversion, and translocation of sequences. In the past 10 years, high-throughput short reads have greatly expanded our ability to assay sequence variation due to single nucleotide polymorphisms. However, a recent de novo assembly of a second Drosophila melanogaster reference genome has revealed that short read genotyping methods miss hundreds of structural variants, including those affecting phenotypes. While genomes assembled using highcoverage long reads can achieve high levels of contiguity and completeness, concerns about cost, errors, and low yield have limited widespread adoption of such sequencing approaches. Here we resequenced the reference strain of D. melanogaster (ISO1) on a single Oxford Nanopore MinION flow cell run for 24 hr. Using only reads longer than 1 kb or with at least 30x coverage, we assembled a highly contiguous de novo genome. The addition of inexpensive paired reads and subsequent scaffolding using an optical map technology achieved an assembly with completeness and contiguity comparable to the D. melanogaster reference assembly. Comparison of our assembly to the reference assembly of ISO1 uncovered a number of structural variants (SVs), including novel LTR transposable element insertions and duplications affecting genes with developmental, behavioral, and metabolic functions. Collectively, these SVs provide a snapshot of the dynamics of genome evolution. Furthermore, our assembly and comparison to the D. melanogaster reference genome demonstrates that high-quality de novo assembly of reference genomes and comprehensive variant discovery using such assemblies are now possible by a single lab for under $1,000 (USD).", "date": "2018-10-01T00:00:00Z", "citationCount": 70, "authors": [ { "name": "Solares E.A." }, { "name": "Chakraborty M." }, { "name": "Miller D.E." }, { "name": "Kalsow S." }, { "name": "Hall K." }, { "name": "Perera A.G." }, { "name": "Emerson J.J." }, { "name": "Scott Hawley R." } ], "journal": "G3: Genes, Genomes, Genetics" } } ], "credit": [ { "name": "Mahul Chakraborty", "email": null, "url": "https://mahulchakraborty.wordpress.com/", "orcidid": "https://orcid.org/0000-0003-2414-9187", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Kigaard", "additionDate": "2021-05-27T09:04:45Z", "lastUpdate": "2025-06-18T12:17:20.983962Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-CZ", "Keiler_Collier" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SKM", "description": "Stress Knowledge Map: A compilation of knowledge on mechanisms underlying responses of plants to stress, the so called stress signalling network.", "homepage": "https://skm.nib.si/", "biotoolsID": "skm", "biotoolsCURIE": "biotools:skm", "version": [], "otherID": [], "relation": [ { "biotoolsID": "gomapman", "type": "uses" }, { "biotoolsID": "newt-ve", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2299", "term": "Gene name" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_3619", "term": "sif" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [ { "data": { "uri": "http://edamontology.org/data_0950", "term": "Mathematical model" }, "format": [ { "uri": "http://edamontology.org/format_2585", "term": "SBML" }, { "uri": "http://edamontology.org/format_3692", "term": "SBGN-ML" }, { "uri": "http://edamontology.org/format_3619", "term": "sif" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "ELIXIR-SI", "Plant Systems Biology" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Slovenia" ], "elixirCommunity": [ "Plant Sciences" ], "link": [ { "url": "https://skm.nib.si/contact", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [ { "url": "https://skm.nib.si/documentation", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/j.xplc.2024.100920", "pmid": "38616489", "pmcid": null, "type": [ "Primary" ], "version": null, "note": "Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses", "metadata": { "title": "Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses", "abstract": "Stress Knowledge Map (SKM; https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical, signaling, and regulatory molecular interactions in plants: a highly curated model of plant stress signaling (PSS; 543 reactions) and a large comprehensive knowledge network (488 390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entry point for investigations of plant stress response and related growth trade-offs, as well as interactive explorations of current knowledge. PSS is also formulated as a qualitative and quantitative model for systems biology and thus represents a starting point for a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation and design of validation experiments, or to gain new insights into experimental observations in plant biology.", "date": "2024-06-10T00:00:00Z", "citationCount": 8, "authors": [ { "name": "Bleker C." }, { "name": "Ramsak" }, { "name": "Bittner A." }, { "name": "Podpecan V." }, { "name": "Zagorscak M." }, { "name": "Wurzinger B." }, { "name": "Baebler" }, { "name": "Petek M." }, { "name": "Kriznik M." }, { "name": "van Dieren A." }, { "name": "Gruber J." }, { "name": "Afjehi-Sadat L." }, { "name": "Weckwerth W." }, { "name": "Zupanic A." }, { "name": "Teige M." }, { "name": "Vothknecht U.C." }, { "name": "Gruden K." } ], "journal": "Plant Communications" } } ], "credit": [ { "name": "National Institute of Biology, Department of Biotechnology and Systems Biology", "email": null, "url": "http://www.nib.si/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Carissa Bleker", "email": "carissarobyn.bleker@nib.si", "url": null, "orcidid": "https://orcid.org/0000-0003-1617-7145", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Kristina Gruden", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Živa Ramšak", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Vid Podpečan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null } ], "owner": "carissa", "additionDate": "2022-05-16T13:26:15.720803Z", "lastUpdate": "2025-06-18T12:10:26.465410Z", "editPermission": { "type": "group", "authors": [ "zagor" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "QUAST", "description": "QUAST stands for QUality ASsessment Tool. \nIt evaluates a quality of genome assemblies by computing various metrics and providing nice reports.", "homepage": "http://quast.sourceforge.net/quast", "biotoolsID": "quast", "biotoolsCURIE": "biotools:quast", "version": [ "v.5.3.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_3180", "term": "Sequence assembly validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [], "note": "# Running quast on a eukaryotic genome", "cmd": "quast -ek assembly.fa --out output_prefix" } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Perl", "Python", "C" ], "license": "GPL-2.0", "collectionID": [ "ONTeater" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/ablab/quast", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/ablab/quast/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [ { "url": "http://quast.bioinf.spbau.ru/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btt086", "pmid": "23422339", "pmcid": "PMC3624806", "type": [], "version": null, "note": null, "metadata": { "title": "QUAST: Quality assessment tool for genome assemblies", "abstract": "Limitations of genome sequencing techniques have led to dozens of assembly algorithms, none of which is perfect. A number of methods for comparing assemblers have been developed, but none is yet a recognized benchmark. Further, most existing methods for comparing assemblies are only applicable to new assemblies of finished genomes; the problem of evaluating assemblies of previously unsequenced species has not been adequately considered. Here, we present QUAST - a quality assessment tool for evaluating and comparing genome assemblies. This tool improves on leading assembly comparison software with new ideas and quality metrics. QUAST can evaluate assemblies both with a reference genome, as well as without a reference. QUAST produces many reports, summary tables and plots to help scientists in their research and in their publications. In this study, we used QUAST to compare several genome assemblers on three datasets. QUAST tables and plots for all of them are available in the Supplementary Material, and interactive versions of these reports are on the QUAST website. © 2013 The Author.", "date": "2013-04-15T00:00:00Z", "citationCount": 6872, "authors": [ { "name": "Gurevich A." }, { "name": "Saveliev V." }, { "name": "Vyahhi N." }, { "name": "Tesler G." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "QUAST Support", "email": "quast.support@cab.spbu.ru", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "seqwiki_import", "additionDate": "2017-01-13T13:16:01Z", "lastUpdate": "2025-06-18T11:53:52.861712Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-CZ", "Keiler_Collier" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Racon", "description": "Consensus module for raw de novo DNA assembly of long uncorrected reads\n\nRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.", "homepage": "https://github.com/isovic/racon", "biotoolsID": "Racon", "biotoolsCURIE": "biotools:Racon", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0525", "term": "Genome assembly" }, { "uri": "http://edamontology.org/operation_0523", "term": "Mapping assembly" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_2573", "term": "SAM" } ] }, { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": "# The mapping file can be generated with any mapping program - eg, bwa-mem or minimap2.\n# The following is an example using minimap2 with ONT data\nminimap2 assembly.fa-ax map-ont reads.fa > mapped_reads.sam", "cmd": "racon -u reads.fa mapped_reads.sam assembly.fa > assembly_racon.fa" } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3673", "term": "Whole genome sequencing" }, { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "C++", "Python" ], "license": "MIT", "collectionID": [ "ONTeater" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/isovic/racon", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/isovic/racon/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.3390/plants8080270", "pmid": "31390788", "pmcid": "PMC6724115", "type": [], "version": null, "note": null, "metadata": { "title": "Constructing a reference genome in a single lab: The possibility to use oxford nanopore technology", "abstract": "The whole genome sequencing (WGS) has become a crucial tool in understanding genome structure and genetic variation. The MinION sequencing of Oxford Nanopore Technologies (ONT) is an excellent approach for performing WGS and it has advantages in comparison with other Next-Generation Sequencing (NGS): It is relatively inexpensive, portable, has simple library preparation, can be monitored in real-time, and has no theoretical limits on reading length. Sorghum bicolor (L.) Moench is diploid (2n = 2x = 20) with a genome size of about 730 Mb, and its genome sequence information is released in the Phytozome database. Therefore, sorghum can be used as a good reference. However, plant species have complex and large genomes when compared to animals or microorganisms. As a result, complete genome sequencing is difficult for plant species. MinION sequencing that produces long-reads can be an excellent tool for overcoming the weak assembly of short-reads generated from NGS by minimizing the generation of gaps or covering the repetitive sequence that appears on the plant genome. Here, we conducted the genome sequencing for S. bicolor cv. BTx623 while using the MinION platform and obtained 895,678 reads and 17.9 gigabytes (Gb) (ca. 25× coverage of reference) from long-read sequence data. A total of 6124 contigs (covering 45.9%) were generated from Canu, and a total of 2661 contigs (covering 50%) were generated from Minimap and Miniasm with a Racon through a de novo assembly using two different tools and mapped assembled contigs against the sorghum reference genome. Our results provide an optimal series of long-read sequencing analysis for plant species while using the MinION platform and a clue to determine the total sequencing scale for optimal coverage that is based on various genome sizes.", "date": "2019-08-01T00:00:00Z", "citationCount": 13, "authors": [ { "name": "Lee Y.G." }, { "name": "Choi S.C." }, { "name": "Kang Y." }, { "name": "Kim K.M." }, { "name": "Kang C.-S." }, { "name": "Kim C." } ], "journal": "Plants" } } ], "credit": [ { "name": "Chon-Sik Kang", "email": "cskang@korea.kr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Changsoo Kim", "email": "changsookim@cnu.ac.kr", "url": null, "orcidid": "https://orcid.org/0000-0002-3596-2934", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Pub2Tools", "additionDate": "2019-11-14T18:44:38Z", "lastUpdate": "2025-06-18T11:42:42.378216Z", "editPermission": { "type": "public", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Flye", "description": "Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.", "homepage": "https://github.com/fenderglass/Flye", "biotoolsID": "Flye", "biotoolsCURIE": "biotools:Flye", "version": [ "2.9.6" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0525", "term": "Genome assembly" }, { "uri": "http://edamontology.org/operation_0524", "term": "De-novo assembly" }, { "uri": "http://edamontology.org/operation_0523", "term": "Mapping assembly" }, { "uri": "http://edamontology.org/operation_3730", "term": "Cross-assembly" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3673", "term": "Whole genome sequencing" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "C++", "Python", "C" ], "license": "BSD-3-Clause", "collectionID": [ "ONTeater" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/fenderglass/Flye/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://github.com/mikolmogorov/Flye", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1099/mgen.0.000294", "pmid": "31483244", "pmcid": "PMC6807382", "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes", "abstract": "Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome assembly. Long-read sequencing greatly assists with resolving complex bacterial genomes, particularly when combined with short-read Illumina data (hybrid assembly). However, it is not clear how different long-read sequencing methods affect hybrid assembly accuracy. Relative automation of the assembly process is also crucial to facilitating high-throughput complete bacterial genome reconstruction, avoiding multiple bespoke filtering and data manipulation steps. In this study, we compared hybrid assemblies for 20 bacterial isolates, including two reference strains, using Illumina sequencing and long reads from either Oxford Nanopore Technologies (ONT) or SMRT Pacific Biosciences (PacBio) sequencing platforms. We chose isolates from the family Enterobacteriaceae, as these frequently have highly plastic, repetitive genetic structures, and complete genome reconstruction for these species is relevant for a precise understanding of the epidemiology of antimicrobial resistance. We de novo assembled genomes using the hybrid assembler Unicycler and compared different read processing strategies, as well as comparing to long-read-only assembly with Flye followed by short-read polishing with Pilon. Hybrid assembly with either PacBio or ONT reads facilitated high-quality genome reconstruction, and was superior to the longread assembly and polishing approach evaluated with respect to accuracy and completeness. Combining ONT and Illumina reads fully resolved most genomes without additional manual steps, and at a lower consumables cost per isolate in our setting. Automated hybrid assembly is a powerful tool for complete and accurate bacterial genome assembly.", "date": "2019-01-01T00:00:00Z", "citationCount": 166, "authors": [ { "name": "De Maio N." }, { "name": "Shaw L.P." }, { "name": "Hubbard A." }, { "name": "George S." }, { "name": "Sanderson N.D." }, { "name": "Swann J." }, { "name": "Wick R." }, { "name": "Oun M.A." }, { "name": "Stubberfield E." }, { "name": "Hoosdally S.J." }, { "name": "Crook D.W." }, { "name": "Peto T.E.A." }, { "name": "Sheppard A.E." }, { "name": "Bailey M.J." }, { "name": "Read D.S." }, { "name": "Anjum M.F." }, { "name": "Sarah Walker A." }, { "name": "Stoesser N." } ], "journal": "Microbial Genomics" } }, { "doi": "10.1038/s41587-019-0072-8", "pmid": "30936562", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Assembly of long, error-prone reads using repeat graphs", "abstract": "Accurate genome assembly is hampered by repetitive regions. Although long single molecule sequencing reads are better able to resolve genomic repeats than short-read data, most long-read assembly algorithms do not provide the repeat characterization necessary for producing optimal assemblies. Here, we present Flye, a long-read assembly algorithm that generates arbitrary paths in an unknown repeat graph, called disjointigs, and constructs an accurate repeat graph from these error-riddled disjointigs. We benchmark Flye against five state-of-the-art assemblers and show that it generates better or comparable assemblies, while being an order of magnitude faster. Flye nearly doubled the contiguity of the human genome assembly (as measured by the NGA50 assembly quality metric) compared with existing assemblers.", "date": "2019-05-01T00:00:00Z", "citationCount": 3077, "authors": [ { "name": "Kolmogorov M." }, { "name": "Yuan J." }, { "name": "Lin Y." }, { "name": "Pevzner P.A." } ], "journal": "Nature Biotechnology" } }, { "doi": "10.1038/s41592-020-00971-x", "pmid": "33020656", "pmcid": "PMC10699202", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "metaFlye: scalable long-read metagenome assembly using repeat graphs", "abstract": "Long-read sequencing technologies have substantially improved the assemblies of many isolate bacterial genomes as compared to fragmented short-read assemblies. However, assembling complex metagenomic datasets remains difficult even for state-of-the-art long-read assemblers. Here we present metaFlye, which addresses important long-read metagenomic assembly challenges, such as uneven bacterial composition and intra-species heterogeneity. First, we benchmarked metaFlye using simulated and mock bacterial communities and show that it consistently produces assemblies with better completeness and contiguity than state-of-the-art long-read assemblers. Second, we performed long-read sequencing of the sheep microbiome and applied metaFlye to reconstruct 63 complete or nearly complete bacterial genomes within single contigs. Finally, we show that long-read assembly of human microbiomes enables the discovery of full-length biosynthetic gene clusters that encode biomedically important natural products.", "date": "2020-11-01T00:00:00Z", "citationCount": 511, "authors": [ { "name": "Kolmogorov M." }, { "name": "Bickhart D.M." }, { "name": "Behsaz B." }, { "name": "Gurevich A." }, { "name": "Rayko M." }, { "name": "Shin S.B." }, { "name": "Kuhn K." }, { "name": "Yuan J." }, { "name": "Polevikov E." }, { "name": "Smith T.P.L." }, { "name": "Pevzner P.A." } ], "journal": "Nature Methods" } } ], "credit": [ { "name": "Mikhail Kolmogorov", "email": "fenderglass@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Support" ], "note": null }, { "name": "Yu Lin", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Jeffrey Yuan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "Pub2Tools", "additionDate": "2019-11-14T20:08:20Z", "lastUpdate": "2025-06-18T10:20:03.775603Z", "editPermission": { "type": "public", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "BOLD (Barcode of Life Database)", "description": "An interactive gateway designed for the tracking and dissemination of DNA barcode reference data. 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Concomitantly, high-throughput sequencing and functional genomics have generated genetic variants at an unprecedented scale. However, efficient tools and resources are needed to link disparate data types—to ‘map’ variants onto protein structures, to better understand how the variation causes disease, and thereby design therapeutics. Here we present the Genomics 2 Proteins portal (https://g2p.broadinstitute.org/): a human proteome-wide resource that maps 20,076,998 genetic variants onto 42,413 protein sequences and 77,923 structures, with a comprehensive set of structural and functional features. Additionally, the Genomics 2 Proteins portal allows users to interactively upload protein residue-wise annotations (for example, variants and scores) as well as the protein structure beyond databases to establish the connection between genomics to proteins. The portal serves as an easy-to-use discovery tool for researchers and scientists to hypothesize the structure–function relationship between natural or synthetic variations and their molecular phenotypes.", "date": "2024-10-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Kwon S." }, { "name": "Safer J." }, { "name": "Nguyen D.T." }, { "name": "Hoksza D." }, { "name": "May P." }, { "name": "Arbesfeld J.A." }, { "name": "Rubin A.F." }, { "name": "Campbell A.J." }, { "name": "Burgin A." }, { "name": "Iqbal S." } ], "journal": "Nature Methods" } } ], "credit": [], "owner": "unethical", "additionDate": "2025-06-15T04:45:08.927267Z", "lastUpdate": "2025-06-15T04:51:27.735002Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "mzspeclib", "description": "A python reference implementation of the mzSpecLib spectral library format.", "homepage": "https://github.com/HUPO-PSI/mzspeclib-py", "biotoolsID": "mzspeclib", "biotoolsCURIE": "biotools:mzspeclib", "version": [ "1.0.5" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_4039", "term": "MSP" }, { "uri": "http://edamontology.org/format_3651", "term": "MGF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [] } ], "note": null, "cmd": "mzspeclib convert" }, { "operation": [ { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" } ], "operatingSystem": [], "language": [ "Python" ], "license": "APSL-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Interoperability" ], "elixirNode": [], "elixirCommunity": [ "Proteomics", "Metabolomics" ], "link": [ { "url": "https://www.psidev.info/", "type": [ "Discussion forum" ], "note": null }, { "url": "https://github.com/HUPO-PSI/mzspeclib-py", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/HUPO-PSI/mzspeclib-py", "type": "Source code", "note": null, "version": null }, { "url": "https://pypi.org/project/mzspeclib/", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "https://hupo-psi.github.io/mzSpecLib/", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.analchem.4c04091", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF", "abstract": "Mass spectral libraries are collections of reference spectra, usually associated with specific analytes from which the spectra were generated, that are used for further downstream analysis of new spectra. There are many different formats used for encoding spectral libraries, but none have undergone a standardization process to ensure broad applicability to many applications. As part of the Human Proteome Organization Proteomics Standards Initiative (PSI), we have developed a standardized format for encoding spectral libraries, called mzSpecLib (https://psidev.info/mzSpecLib). It is primarily a data model that flexibly encodes metadata about the library entries using the extensible PSI-MS controlled vocabulary and can be encoded in and converted between different serialization formats. We have also developed a standardized data model and serialization for fragment ion peak annotations, called mzPAF (https://psidev.info/mzPAF). It is defined as a separate standard, since it may be used for other applications besides spectral libraries. The mzSpecLib and mzPAF standards are compatible with existing PSI standards such as ProForma 2.0 and the Universal Spectrum Identifier. The mzSpecLib and mzPAF standards have been primarily defined for peptides in proteomics applications with basic small molecule support. They could be extended in the future to other fields that need to encode spectral libraries for nonpeptidic analytes.", "date": "2024-11-19T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Klein J." }, { "name": "Lam H." }, { "name": "Mak T.D." }, { "name": "Bittremieux W." }, { "name": "Perez-Riverol Y." }, { "name": "Gabriels R." }, { "name": "Shofstahl J." }, { "name": "Hecht H." }, { "name": "Binz P.-A." }, { "name": "Kawano S." }, { "name": "Van Den Bossche T." }, { "name": "Carver J." }, { "name": "Neely B.A." }, { "name": "Mendoza L." }, { "name": "Suomi T." }, { "name": "Claeys T." }, { "name": "Payne T." }, { "name": "Schulte D." }, { "name": "Sun Z." }, { "name": "Hoffmann N." }, { "name": "Zhu Y." }, { "name": "Neumann S." }, { "name": "Jones A.R." }, { "name": "Bandeira N." }, { "name": "Vizcaino J.A." }, { "name": "Deutsch E.W." } ], "journal": "Analytical Chemistry" } } ], "credit": [], "owner": "recetox-specdatri", "additionDate": "2025-06-12T11:47:48.641345Z", "lastUpdate": "2025-06-12T11:57:26.484553Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Askomics", "description": "AskOmics is a visual SPARQL query interface supporting both intuitive data integration and querying while shielding the user from most of the technical difficulties underlying RDF and SPARQL", "homepage": "https://github.com/askomics", "biotoolsID": "askomics", "biotoolsCURIE": "biotools:askomics", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1255", "term": "Sequence features" }, "format": [ { "uri": "http://edamontology.org/format_2305", "term": "GFF" } ] }, { "data": { "uri": "http://edamontology.org/data_2353", "term": "Ontology data" }, "format": [ { "uri": "http://edamontology.org/format_2376", "term": "RDF format" } ] }, { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" }, { "uri": "http://edamontology.org/format_2376", "term": "RDF format" } ] } ], "note": "Visualization graph", "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python" ], "license": "AGPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/askomics/askomics/releases", "type": "Software package", "note": null, "version": null }, { "url": "https://github.com/askomics/askomics-docker-compose/archive/master.tar.gz", "type": "Container file", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/askomics/askomics", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "Olivier Dameron", "email": "olivier.dameron@irisa.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Olivier Filangi", "email": "olivier.filangi@inra.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Anthony Bretaudeau", "email": "anthony.bretaudeau@irisa.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mboudet", "additionDate": "2017-12-12T17:28:02Z", "lastUpdate": "2025-06-09T11:52:30.706337Z", "editPermission": { "type": "group", "authors": [ "jgot" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Virtual Imaging Platform", "description": "VIP is a web portal for medical imaging applications. It allows users to access scientific applications as a service (directly through the web browser with no installation required), as well as distributed computing resources in a transparent manner. It exploits the resources available in the biomed virtual organization of the EGI e-infrastructure to offer an open service to researchers worldwide.", "homepage": "https://vip.creatis.insa-lyon.fr", "biotoolsID": "virtual_imaging_platform", "biotoolsCURIE": "biotools:virtual_imaging_platform", "version": [ "3.0.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Bioinformatics portal" ], "topic": [], "operatingSystem": [], "language": [ "Java" ], "license": "CECILL-B", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://vip.creatis.insa-lyon.fr/", "type": [ "Service" ], "note": null } ], "download": [ { "url": "https://github.com/virtual-imaging-platform/", "type": "Source code", "note": null, "version": "3.0.1" } ], "documentation": [ { "url": "https://github.com/virtual-imaging-platform/VIP-portal/wiki", "type": [ "Other" ], "note": null } ], "publication": [ { "doi": "10.1109/tmi.2012.2220154", "pmid": "23014715", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "A virtual imaging platform for multi-modality medical image simulation", "abstract": "This paper presents the Virtual Imaging Platform (VIP), a platform accessible at http://vip.creatis.insa-lyon.fr to facilitate the sharing of object models and medical image simulators, and to provide access to distributed computing and storage resources. A complete overview is presented, describing the ontologies designed to share models in a common repository, the workflow template used to integrate simulators, and the tools and strategies used to exploit computing and storage resources. Simulation results obtained in four image modalities and with different models show that VIP is versatile and robust enough to support large simulations. The platform currently has 200 registered users who consumed 33 years of CPU time in 2011. © 1982-2012 IEEE.", "date": "2013-01-10T00:00:00Z", "citationCount": 88, "authors": [ { "name": "Glatard T." }, { "name": "Lartizien C." }, { "name": "Gibaud B." }, { "name": "Da Silva R.F." }, { "name": "Forestier G." }, { "name": "Cervenansky F." }, { "name": "Alessandrini M." }, { "name": "Benoit-Cattin H." }, { "name": "Bernard O." }, { "name": "Camarasu-Pop S." }, { "name": "Cerezo N." }, { "name": "Clarysse P." }, { "name": "Gaignard A." }, { "name": "Hugonnard P." }, { "name": "Liebgott H." }, { "name": "Marache S." }, { "name": "Marion A." }, { "name": "Montagnat J." }, { "name": "Tabary J." }, { "name": "Friboulet D." } ], "journal": "IEEE Transactions on Medical Imaging" } } ], "credit": [], "owner": "sorina.pop", "additionDate": "2023-06-14T13:47:49.064543Z", "lastUpdate": "2025-06-06T11:51:24.125664Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MALDIquant", "description": "MALDIquant is a complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.", "homepage": "https://cran.r-project.org/package=MALDIquant", "biotoolsID": "maldi_quant", "biotoolsCURIE": "biotools:maldi_quant", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3799", "term": "Quantification" }, { "uri": "http://edamontology.org/operation_3860", "term": "Spectrum calculation" }, { "uri": "http://edamontology.org/operation_3215", "term": "Peak detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3682", "term": "imzML metadata file" } ] }, { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3839", "term": "ibd" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3682", "term": "imzML metadata file" } ] }, { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3839", "term": "ibd" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3627", "term": "Mass spectra calibration" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3682", "term": "imzML metadata file" } ] }, { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3839", "term": "ibd" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3682", "term": "imzML metadata file" } ] }, { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3839", "term": "ibd" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/sgibb/MALDIquant/", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/sgibb/MALDIquant/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "http://strimmerlab.org/software/maldiquant/", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [ { "url": "https://cran.r-project.org/web/packages/MALDIquant/MALDIquant.pdf", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bts447", "pmid": "22796955", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Maldiquant: A versatile R package for the analysis of mass spectrometry data", "abstract": "MALDIquant is an R package providing a complete and modular analysis pipeline for quantitative analysis of mass spectrometry data. MALDIquant is specifically designed with application in clinical diagnostics in mind and implements sophisticated routines for importing raw data, preprocessing, non-linear peak alignment and calibration. It also handles technical replicates as well as spectra with unequal resolution. © The Author 2012. Published by Oxford University Press. All rights reserved.", "date": "2012-09-01T00:00:00Z", "citationCount": 499, "authors": [ { "name": "Gibb S." }, { "name": "Strimmer K." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Sebastian Gibb", "email": "mail@sebastiangibb.de", "url": null, "orcidid": "https://orcid.org/0000-0001-7406-4443", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Korbinian Strimmer", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-7917-2056", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "Kigaard", "additionDate": "2021-05-26T20:42:18Z", "lastUpdate": "2025-06-05T11:28:57.497366Z", "editPermission": { "type": "group", "authors": [ "sizhengZhao" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Galaxy Image Analysis", "description": "Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.", "homepage": "https://github.com/BMCV/galaxy-image-analysis", "biotoolsID": "galaxy_image_analysis", "biotoolsCURIE": "biotools:galaxy_image_analysis", "version": [], "otherID": [], "relation": [ { "biotoolsID": "galaxy", "type": "includedIn" }, { "biotoolsID": "segmetrics", "type": "includes" }, { "biotoolsID": "superdsm", "type": "includes" }, { "biotoolsID": "rfove", "type": "includes" }, { "biotoolsID": "giatools", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3727", "term": "OME-TIFF" }, { "uri": "http://edamontology.org/format_3591", "term": "TIFF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] }, { "data": { "uri": "http://edamontology.org/data_0920", "term": "Genotype/phenotype report" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Suite" ], "topic": [ { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [], "license": null, "collectionID": [ "de.NBI", "HD-HuB" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://github.com/BMCV/galaxy-image-analysis", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/j.jbiotec.2017.07.019", "pmid": "28757289", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Workflows for microscopy image analysis and cellular phenotyping", "abstract": "In large scale biological experiments, like high-throughput or high-content cellular screening, the amount and the complexity of images to be analyzed are steadily increasing. To handle and process these images, well defined image processing and analysis steps need to be performed by applying dedicated workflows. Multiple software tools have emerged with the aim to facilitate creation of such workflows by integrating existing methods, tools, and routines, and by adapting them to different applications and questions, as well as making them reusable and interchangeable. In this review, we describe workflow systems for the integration of microscopy image analysis techniques with focus on KNIME and Galaxy.", "date": "2017-11-10T00:00:00Z", "citationCount": 22, "authors": [ { "name": "Wollmann T." }, { "name": "Erfle H." }, { "name": "Eils R." }, { "name": "Rohr K." }, { "name": "Gunkel M." } ], "journal": "Journal of Biotechnology" } } ], "credit": [ { "name": "Thomas Wollmann", "email": "thomas.wollmann@bioquant.uni-heidelberg.de", "url": "https://www.bioquant.uni-heidelberg.de/bmcv", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hdhub", "additionDate": "2017-03-21T13:32:41Z", "lastUpdate": "2025-06-04T09:45:37.769508Z", "editPermission": { "type": "group", "authors": [ "kostrykin" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Arabidopsis Co-expression Tool (ACT)", "description": "The Arabidopsis Coexpression Tool (ACT) is based on the coexpression analysis of 21273 Arabidopsis thaliana genes from gene pair correlation data of 3500 Affymetrix Arabidopsis ATH1 Genome Array Chip microarray samples.", "homepage": "https://www.michalopoulos.net/act/", "biotoolsID": "act", "biotoolsCURIE": "biotools:act", "version": [ "2.6" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2938", "term": "Dendrogram visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1025", "term": "Gene identifier" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3271", "term": "Gene tree" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Greece" ], "elixirCommunity": [ "Plant Sciences" ], "link": [], "download": [], "documentation": [ { "url": "https://www.michalopoulos.net/act2.6/help.php", "type": [ "FAQ" ], "note": null } ], "publication": [ { "doi": "10.3390/genes16030258", "pmid": "40149410", "pmcid": "PMC11942487", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "ACT2.6: Global Gene Coexpression Network in Arabidopsis thaliana Using WGCNA", "abstract": "Background/Objectives: Genes with similar expression patterns across multiple samples are considered coexpressed, and they may participate in similar biological processes or pathways. Gene coexpression networks depict the degree of similarity between the expression profiles of all genes in a set of samples. Gene coexpression tools allow for the prediction of functional gene partners or the assignment of roles to genes of unknown function. Weighted Gene Correlation Network Analysis (WGCNA) is an R package that provides a multitude of functions for constructing and analyzing a weighted or unweighted gene coexpression network. Methods: Previously preprocessed, high-quality gene expression data of 3500 samples of Affymetrix microarray technology from various tissues of the Arabidopsis thaliana plant model species were used to construct a weighted gene coexpression network, using WGCNA. Results: The gene dendrogram was used as the basis for the creation of a new Arabidopsis coexpression tool (ACT) version (ACT2.6). The dendrogram contains 21,273 leaves, each one corresponding to a single gene. Genes that are clustered in the same clade are coexpressed. WGCNA grouped the genes into 27 functional modules, all of which were positively or negatively correlated with specific tissues. Discussion: Genes known to be involved in common metabolic pathways were discovered in the same module. By comparing the current ACT version with the previous one, it was shown that the new version outperforms the old one in discovering the functional connections between gene partners. ACT2.6 is a major upgrade over the previous version and a significant addition to the collection of public gene coexpression tools.", "date": "2025-03-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Zogopoulos V.L." }, { "name": "Papadopoulos K." }, { "name": "Malatras A." }, { "name": "Iconomidou V.A." }, { "name": "Michalopoulos I." } ], "journal": "Genes" } }, { "doi": "10.1016/j.xpro.2022.101208", "pmid": "35243384", "pmcid": "PMC8885756", "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "Gene coexpression analysis in Arabidopsis thaliana based on public microarray data", "abstract": "Coexpressed genes tend to participate in related biological processes. Gene coexpression analysis allows the discovery of functional gene partners or the assignment of biological roles to genes of unknown function. In this protocol, we describe the steps necessary to create a gene coexpression tree for Arabidopsis thaliana, using publicly available Affymetrix CEL microarray data. Because the computational analysis described here is highly dependent on sample quality, we detail an automatic quality control approach. For complete details on the use and execution of this protocol, please refer to Zogopoulos et al. (2021).", "date": "2022-03-18T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Zogopoulos V.L." }, { "name": "Malatras A." }, { "name": "Michalopoulos I." } ], "journal": "STAR Protocols" } }, { "doi": "10.3390/biology11071019", "pmid": "36101400", "pmcid": "PMC9312353", "type": [ "Review" ], "version": null, "note": null, "metadata": { "title": "Approaches in Gene Coexpression Analysis in Eukaryotes", "abstract": "Gene coexpression analysis constitutes a widely used practice for gene partner identification and gene function prediction, consisting of many intricate procedures. The analysis begins with the collection of primary transcriptomic data and their preprocessing, continues with the calculation of the similarity between genes based on their expression values in the selected sample dataset and results in the construction and visualisation of a gene coexpression network (GCN) and its evaluation using biological term enrichment analysis. As gene coexpression analysis has been studied ex-tensively, we present most parts of the methodology in a clear manner and the reasoning behind the selection of some of the techniques. In this review, we offer a comprehensive and comprehensi-ble account of the steps required for performing a complete gene coexpression analysis in eukary-otic organisms. We comment on the use of RNA‐Seq vs. microarrays, as well as the best practices for GCN construction. Furthermore, we recount the most popular webtools and standalone applications performing gene coexpression analysis, with details on their methods, features and outputs.", "date": "2022-07-01T00:00:00Z", "citationCount": 11, "authors": [ { "name": "Zogopoulos V.L." }, { "name": "Saxami G." }, { "name": "Malatras A." }, { "name": "Papadopoulos K." }, { "name": "Tsotra I." }, { "name": "Iconomidou V.A." }, { "name": "Michalopoulos I." } ], "journal": "Biology" } }, { "doi": "10.1093/nar/gkl204", "pmid": "16845059", "pmcid": "PMC1538833", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Arabidopsis Co-expression Tool (ACT): Web server tools for microarray-based gene expression analysis", "abstract": "The Arabidopsis Co-expression Tool, ACT, ranks the genes across a large microarray dataset according to how closely their expression follows the expression of a query gene. A database stores pre-calculated co-expression results for ∼21 800 genes based on data from over 300 arrays. These results can be corroborated by calculation of co-expression results for user-defined sub-sets of arrays or experiments from the NASC/GARNet array dataset. Clique Finder (CF) identifies groups of genes which are consistently co-expressed with each other across a user-defined co-expression list. The parameters can be altered easily to adjust cluster size and the output examined for optimal inclusion of genes with known biological roles. Alternatively, a Scatter Plot tool displays the correlation coefficients for all genes against two user-selected queries on a scatter plot which can be useful for visual identification of clusters of genes with similar r-values. User-input groups of genes can be highlighted on the scatter plots. Inclusion of genes with known biology in sets of genes identified using CF and Scatter Plot tools allows inferences to be made about the roles of the other genes in the set and both tools can therefore be used to generate short lists of genes for further characterization. ACT is freely available at www.Arabidopsis.leeds.ac.uk/ACT. © The Author 2006. Published by Oxford University Press. All rights reserved.", "date": "2006-07-01T00:00:00Z", "citationCount": 130, "authors": [ { "name": "Manfield I.W." }, { "name": "Jen C.-H." }, { "name": "Pinney J.W." }, { "name": "Michalopoulos I." }, { "name": "Bradford J.R." }, { "name": "Gilmartin P.M." }, { "name": "Westhead D.R." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1111/j.1365-313x.2006.02681.x", "pmid": "16623895", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Arabidopsis co-expression tool (ACT): A WWW-based tool and database for microarray-based gene expression analysis", "abstract": "We present a new WWW-based tool for plant gene analysis, the Arabidopsis Co-Expression Tool (ACT), based on a large Arabidopsis thaliana microarray data set obtained from the Nottingham Arabidopsis Stock Centre. The co-expression analysis tool allows users to identify genes whose expression patterns are correlated across selected experiments or the complete data set. Results are accompanied by estimates of the statistical significance of the correlation relationships, expressed as probability (P) and expectation (E) values. Additionally, highly ranked genes on a correlation list can be examined using the novel CLIQUE FINDER tool to determine the sets of genes most likely to be regulated in a similar manner. In combination, these tools offer three levels of analysis: creation of correlation lists of co-expressed genes, refinement of these lists using two-dimensional scatter plots, and dissection into cliques of co-regulated genes. We illustrate the applications of the software by analysing genes encoding functionally related proteins, as well as pathways involved in plant responses to environmental stimuli. These analyses demonstrate novel biological relationships underlying the observed gene co-expression patterns. To demonstrate the ability of the software to develop testable hypotheses on gene function within a defined biological process we have used the example of cell wall biosynthesis genes. The resource is freely available at http://www.arabidopsis.leeds.ac.uk/ACT/. © 2006 The Authors.", "date": "2006-04-01T00:00:00Z", "citationCount": 65, "authors": [ { "name": "Jen C.-H." }, { "name": "Manfield I.W." }, { "name": "Michalopoulos I." }, { "name": "Pinney J.W." }, { "name": "Willats W.G.T." }, { "name": "Gilmartin P.M." }, { "name": "Westhead D.R." } ], "journal": "Plant Journal" } }, { "doi": "10.1016/j.isci.2021.102848", "pmid": "34381973", "pmcid": "PMC8334378", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana", "abstract": "Gene coexpression analysis refers to the discovery of sets of genes which exhibit similar expression patterns across multiple transcriptomic data sets, such as microarray experiment data of public repositories. Arabidopsis Coexpression Tool (ACT), a gene coexpression analysis web tool for Arabidopsis thaliana, identifies genes which are correlated to a driver gene. Primary microarray data from ATH1 Affymetrix platform were processed with Single-Channel Array Normalization algorithm and combined to produce a coexpression tree which contains ∼21,000 A. thaliana genes. ACT was developed to present subclades of coexpressed genes, as well as to perform gene set enrichment analysis, being unique in revealing enriched transcription factors targeting coexpressed genes. ACT offers a simple and user-friendly interface producing working hypotheses which can be experimentally verified for the discovery of gene partnership, pathway membership, and transcriptional regulation. ACT analyses have been successful in identifying not only genes with coordinated ubiquitous expressions but also genes with tissue-specific expressions.", "date": "2021-08-20T00:00:00Z", "citationCount": 15, "authors": [ { "name": "Zogopoulos V.L." }, { "name": "Saxami G." }, { "name": "Malatras A." }, { "name": "Angelopoulou A." }, { "name": "Jen C.-H." }, { "name": "Duddy W.J." }, { "name": "Daras G." }, { "name": "Hatzopoulos P." }, { "name": "Westhead D.R." }, { "name": "Michalopoulos I." } ], "journal": "iScience" } } ], "credit": [ { "name": "David R Westhead", "email": "D.R.Westhead@leeds.ac.uk", "url": "https://biologicalsciences.leeds.ac.uk/molecular-and-cellular-biology/staff/154/professor-david-r-westhead", "orcidid": "https://orcid.org/0000-0002-0519-3820", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Ioannis Michalopoulos", "email": "imichalop@bioacademy.gr", "url": "https://www.michalopoulos.net/", "orcidid": "https://orcid.org/0000-0001-8991-8712", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "imichalop@bioacademy.gr", "additionDate": "2017-02-10T14:14:47Z", "lastUpdate": "2025-06-04T05:50:14.941224Z", "editPermission": { "type": "private", "authors": [ "imichalop@bioacademy.gr" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CNSistent", "description": "Imputation, consistent segmentation, statistical analysis, and visualization of copy number profiles.", "homepage": "https://cnsistent.readthedocs.io", "biotoolsID": "cnsistent", "biotoolsCURIE": "biotools:cnsistent", "version": [ "0.7.4" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3958", "term": "Copy number variation" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" } ], "operatingSystem": [], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bitbucket.org/schwarzlab/cnsistent.git", "type": "Source code", "note": null, "version": null }, { "url": "https://pypi.org/project/CNSistent/", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "https://cnsistent.readthedocs.io/", "type": [ "Command-line options", "API documentation", "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1101/2024.12.23.630118", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Adam Streck", "email": "adam.streck@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0002-7302-0147", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "AdamStreck", "additionDate": "2025-06-03T11:42:31.433057Z", "lastUpdate": "2025-06-03T11:54:45.306699Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SAMtools", "description": "SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.", "homepage": "http://www.htslib.org/", "biotoolsID": "samtools", "biotoolsCURIE": "biotools:samtools", "version": [ "1.0", "1.1", "1.2", "1.3", "1.3.1", "1.4", "1.4.1", "1.5", "1.6", "1.7", "1.8", "1.9", "1.10", "1.11", "1.12", "1.13", "1.14", "1.15", "1.15.1", "1.16", "1.16.1", "1.17", "1.18", "1.19", "1.19.1", "1.19.2", "1.20", "1.21", "1.22" ], "otherID": [], "relation": [ { "biotoolsID": "htslib", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" }, { "uri": "http://edamontology.org/operation_3096", "term": "Data editing" }, { "uri": "http://edamontology.org/operation_1812", "term": "Data parsing" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_0335", "term": "Data formatting" }, { "uri": "http://edamontology.org/operation_3802", "term": "Data sorting" }, { "uri": "http://edamontology.org/operation_3695", "term": "Data filtering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_2573", "term": "SAM" }, { "uri": "http://edamontology.org/format_3462", "term": "CRAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_2573", "term": "SAM" }, { "uri": "http://edamontology.org/format_3462", "term": "CRAM" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Suite", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C" ], "license": "MIT", "collectionID": [ "Rare Disease", "Animal and Crop Genomics", "SAMtools" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/samtools/samtools", "type": [ "Repository" ], "note": null }, { "url": "http://www.htslib.org/support/#lists", "type": [ "Mailing list" ], "note": null }, { "url": "https://github.com/samtools/samtools/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "http://www.htslib.org/download/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.htslib.org/doc/#howtos", "type": [ "Other" ], "note": "HowTos for samtools" }, { "url": "http://www.htslib.org/doc/#manual-pages", "type": [ "User manual" ], "note": null }, { "url": "http://www.htslib.org/download/", "type": [ "Installation instructions" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btp352", "pmid": "19505943", "pmcid": "PMC2723002", "type": [ "Primary" ], "version": null, "note": "The Sequence Alignment/Map format and SAMtools.", "metadata": { "title": "The Sequence Alignment/Map format and SAMtools", "abstract": "Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAM tools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. © 2009 The Author(s).", "date": "2009-08-01T00:00:00Z", "citationCount": 42239, "authors": [ { "name": "Li H." }, { "name": "Handsaker B." }, { "name": "Wysoker A." }, { "name": "Fennell T." }, { "name": "Ruan J." }, { "name": "Homer N." }, { "name": "Marth G." }, { "name": "Abecasis G." }, { "name": "Durbin R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/gigascience/giab008", "pmid": "33590861", "pmcid": "PMC7931819", "type": [ "Primary" ], "version": null, "note": "Twelve years of SAMtools and BCFtools.", "metadata": { "title": "Twelve years of SAMtools and BCFtools", "abstract": "Background: SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. Findings: The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Conclusion: Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.", "date": "2021-02-01T00:00:00Z", "citationCount": 6224, "authors": [ { "name": "Danecek P." }, { "name": "Bonfield J.K." }, { "name": "Liddle J." }, { "name": "Marshall J." }, { "name": "Ohan V." }, { "name": "Pollard M.O." }, { "name": "Whitwham A." }, { "name": "Keane T." }, { "name": "McCarthy S.A." }, { "name": "Davies R.M." } ], "journal": "GigaScience" } }, { "doi": "10.1093/bioinformatics/btr509", "pmid": "21903627", "pmcid": "PMC3198575", "type": [], "version": null, "note": null, "metadata": { "title": "A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data", "abstract": "Motivation: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample low-coverage sequencing or somatic mutation discovery). These applications press for the development of new methods for analyzing sequence data with uncertainty. Results: We present a statistical framework for calling SNPs, discovering somatic mutations, inferring population genetical parameters and performing association tests directly based on sequencing data without explicit genotyping or linkage-based imputation. On real data, we demonstrate that our method achieves comparable accuracy to alternative methods for estimating site allele count, for inferring allele frequency spectrum and for association mapping. We also highlight the necessity of using symmetric datasets for finding somatic mutations and confirm that for discovering rare events, mismapping is frequently the leading source of errors. © The Author 2011. Published by Oxford University Press. All rights reserved.", "date": "2011-11-01T00:00:00Z", "citationCount": 4405, "authors": [ { "name": "Li H." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Richard Durbin", "email": "rd@sanger.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Wellcome Sanger Institute", "email": "samtools@sanger.ac.uk", "url": "https://www.sanger.ac.uk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider", "Primary contact" ], "note": null }, { "name": "Samtools Help mailing list", "email": null, "url": "https://lists.sourceforge.net/lists/listinfo/samtools-help", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Support" ], "note": null } ], "owner": "awhitwham", "additionDate": "2017-01-13T13:16:12Z", "lastUpdate": "2025-06-03T09:08:10.199446Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE", "animalandcropgenomics", "alice", "awhitwham", "sergitobara" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HTSlib", "description": "The main purpose of HTSlib is to provide access to genomic information files, both alignment data (SAM, BAM, and CRAM formats) and variant data (VCF and BCF formats). The library also provides interfaces to access and index genome reference data in FASTA format and tab-delimited files with genomic coordinates. It is utilized and incorporated into both SAMtools and BCFtools.", "homepage": "http://www.htslib.org/", "biotoolsID": "htslib", "biotoolsCURIE": "biotools:htslib", "version": [ "1.0", "1.1", "1.2", "1.2.1", "1.3", "1.3.1", "1.3.2", "1.4", "1.4.1", "1.5", "1.6", "1.7", "1.8", "1.9", "1.10", "1.10.1", "1.10.2", "1.11", "1.12", "1.13", "1.14", "1.15", "1.15.1", "1.16", "1.17", "1.18", "1.19", "1.20", "1.21", "1.22" ], "otherID": [], "relation": [ { "biotoolsID": "samtools", "type": "usedBy" }, { "biotoolsID": "bcftools", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" }, { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_3462", "term": "CRAM" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_3020", "term": "BCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" }, { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_3462", "term": "CRAM" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_3020", "term": "BCF" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C" ], "license": "MIT", "collectionID": [ "Animal and Crop Genomics" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/samtools/htslib", "type": [ "Repository" ], "note": null }, { "url": "http://www.htslib.org/support/#lists", "type": [ "Mailing list" ], "note": null }, { "url": "https://github.com/samtools/htslib/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "http://www.htslib.org/download/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.htslib.org/doc/#manual-pages", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/gigascience/giab007", "pmid": "33594436", "pmcid": "PMC7931820", "type": [ "Primary" ], "version": null, "note": "HTSlib: C library for reading/writing high-throughput sequencing data.", "metadata": { "title": "HTSlib: C library for reading/writing high-Throughput sequencing data", "abstract": "Background: Since the original publication of the VCF and SAM formats, an explosion of software tools have been created to process these data files. To facilitate this a library was produced out of the original SAMtools implementation, with a focus on performance and robustness. The file formats themselves have become international standards under the jurisdiction of the Global Alliance for Genomics and Health. Findings: We present a software library for providing programmatic access to sequencing alignment and variant formats. It was born out of the widely used SAMtools and BCFtools applications. Considerable improvements have been made to the original code plus many new features including newer access protocols, the addition of the CRAM file format, better indexing and iterators, and better use of threading. Conclusion: Since the original Samtools release, performance has been considerably improved, with a BAM read-write loop running 5 times faster and BAM to SAM conversion 13 times faster (both using 16 threads, compared to Samtools 0.1.19). Widespread adoption has seen HTSlib downloaded >1 million times from GitHub and conda. The C library has been used directly by an estimated 900 GitHub projects and has been incorporated into Perl, Python, Rust, and R, significantly expanding the number of uses via other languages. HTSlib is open source and is freely available from htslib.org under MIT/BSD license.", "date": "2021-02-01T00:00:00Z", "citationCount": 189, "authors": [ { "name": "Bonfield J.K." }, { "name": "Marshall J." }, { "name": "Danecek P." }, { "name": "Li H." }, { "name": "Ohan V." }, { "name": "Whitwham A." }, { "name": "Keane T." } ], "journal": "GigaScience" } } ], "credit": [ { "name": "Wellcome Sanger Institute", "email": "samtools@sanger.ac.uk", "url": "https://www.sanger.ac.uk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider", "Primary contact" ], "note": null }, { "name": "Samtools Help mailing list", "email": null, "url": "https://lists.sourceforge.net/lists/listinfo/samtools-help", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Support" ], "note": null } ], "owner": "awhitwham", "additionDate": "2017-08-20T16:07:58Z", "lastUpdate": "2025-06-03T09:00:20.313887Z", "editPermission": { "type": "group", "authors": [ "animalandcropgenomics", "smoe" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BCFtools", "description": "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. 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It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAM tools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. © 2009 The Author(s).", "date": "2009-08-01T00:00:00Z", "citationCount": 42239, "authors": [ { "name": "Li H." }, { "name": "Handsaker B." }, { "name": "Wysoker A." }, { "name": "Fennell T." }, { "name": "Ruan J." }, { "name": "Homer N." }, { "name": "Marth G." }, { "name": "Abecasis G." }, { "name": "Durbin R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/gigascience/giab008", "pmid": "33590861", "pmcid": "PMC7931819", "type": [ "Primary" ], "version": null, "note": "Twelve years of SAMtools and BCFtools.", "metadata": { "title": "Twelve years of SAMtools and BCFtools", "abstract": "Background: SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. Findings: The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Conclusion: Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.", "date": "2021-02-01T00:00:00Z", "citationCount": 6224, "authors": [ { "name": "Danecek P." }, { "name": "Bonfield J.K." }, { "name": "Liddle J." }, { "name": "Marshall J." }, { "name": "Ohan V." }, { "name": "Pollard M.O." }, { "name": "Whitwham A." }, { "name": "Keane T." }, { "name": "McCarthy S.A." }, { "name": "Davies R.M." } ], "journal": "GigaScience" } } ], "credit": [ { "name": "Wellcome Sanger Institute", "email": "samtools@sanger.ac.uk", "url": "https://www.sanger.ac.uk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Samtools Help mailing list", "email": null, "url": "https://lists.sourceforge.net/lists/listinfo/samtools-help", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Support" ], "note": null } ], "owner": "awhitwham", "additionDate": "2015-08-24T08:35:55Z", "lastUpdate": "2025-06-03T08:59:30.745713Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SynGenes", "description": "SynGenes is a Python class for standardizing Mitochondrial or Chloroplast gene nomenclatures, this class is capable of recognizing and converting the different nomenclature variations into a standardized form.", "homepage": "https://luanrabelo.github.io/SynGenes/", "biotoolsID": "syngenes", "biotoolsCURIE": "biotools:syngenes", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0089", "term": "Ontology and terminology" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" }, { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_3297", "term": "Biotechnology" }, { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://pypi.org/project/SynGenes/", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s12859-024-05781-y", "pmid": "38649820", "pmcid": "PMC11036621", "type": [], "version": null, "note": null, "metadata": { "title": "SynGenes: a Python class for standardizing nomenclatures of mitochondrial and chloroplast genes and a web form for enhancing searches for evolutionary analyses", "abstract": "Background: The reconstruction of the evolutionary history of organisms has been greatly influenced by the advent of molecular techniques, leading to a significant increase in studies utilizing genomic data from different species. However, the lack of standardization in gene nomenclature poses a challenge in database searches and evolutionary analyses, impacting the accuracy of results obtained. Results: To address this issue, a Python class for standardizing gene nomenclatures, SynGenes, has been developed. It automatically recognizes and converts different nomenclature variations into a standardized form, facilitating comprehensive and accurate searches. Additionally, SynGenes offers a web form for individual searches using different names associated with the same gene. The SynGenes database contains a total of 545 gene name variations for mitochondrial and 2485 for chloroplasts genes, providing a valuable resource for researchers. Conclusions: The SynGenes platform offers a solution for standardizing gene nomenclatures of mitochondrial and chloroplast genes and providing a standardized search solution for specific markers in GenBank. Evaluation of SynGenes effectiveness through research conducted on GenBank and PubMedCentral demonstrated its ability to yield a greater number of outcomes compared to conventional searches, ensuring more comprehensive and accurate results. This tool is crucial for accurate database searches, and consequently, evolutionary analyses, addressing the challenges posed by non-standardized gene nomenclature. Graphical abstract: (Figure presented.)", "date": "2024-12-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Rabelo L.P." }, { "name": "Sodre D." }, { "name": "de Sousa R.P.C." }, { "name": "Watanabe L." }, { "name": "Gomes G." }, { "name": "Sampaio I." }, { "name": "Vallinoto M." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Luan Pinto Rabelo", "email": "mvallino@ufpa.br", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Pub2Tools", "additionDate": "2025-05-31T07:43:57.081940Z", "lastUpdate": "2025-05-31T07:43:57.084502Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "PhyloPhlAn", "description": "PhyloPhlAn is a comprehensive and scalable pipeline for phylogenetic profiling of microbial genomes and metagenomes. It enables accurate species- and strain-level classification, including for MAGs, and reconstructs large-scale phylogenies using clade-specific markers.", "homepage": "https://github.com/biobakery/phylophlan", "biotoolsID": "phylophlan", "biotoolsCURIE": "biotools:phylophlan", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0084", "term": "Phylogeny" }, { "uri": "http://edamontology.org/topic_0637", "term": "Taxonomy" }, { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [], "language": [], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "minaHA", "additionDate": "2025-05-23T08:04:37.184569Z", "lastUpdate": "2025-05-30T12:45:17.772561Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "KrakenParser", "description": "KrakenParser is a streamlined toolkit that transforms Kraken-2 taxonomic reports into tidy CSV files, automatically computes relative abundances, and exposes an intuitive API suite for effortless downstream visualization.", "homepage": "https://github.com/PopovIILab/KrakenParser", "biotoolsID": "krakenparser", "biotoolsCURIE": "biotools:krakenparser", "version": [ "0.1.51", "0.1.62", "0.5.0" ], "otherID": [], "relation": [ { "biotoolsID": "krakentools", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Bioinformatics portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0637", "term": "Taxonomy" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python", "Shell" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/PopovIILab/KrakenParser", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/PopovIILab/KrakenParser/wiki", "type": [ "API documentation" ], "note": null }, { "url": "https://github.com/PopovIILab/KrakenParser", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [], "owner": "iliapopov17", "additionDate": "2025-05-30T11:22:28.697447Z", "lastUpdate": "2025-05-30T11:22:28.699989Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MuGVRE", "description": "The MuG Virtual Research Environment is an analysis platform for 3D/4D genomics analyses. 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the exposome and to perform association analyses between exposures and health outcomes.", "homepage": "http://bioconductor.org/packages/release/bioc/html/rexposome.html", "biotoolsID": "rexposome", "biotoolsCURIE": "biotools:rexposome", "version": [ "1.2.0" ], "otherID": [], "relation": [ { "biotoolsID": "omicrexposome", "type": "usedBy" }, { "biotoolsID": "ctdquerier", "type": "usedBy" }, { "biotoolsID": "multidataset", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" } ], "input": [], "output": [], "note": "Load both tsv-like files and data.frame-like R objects..", "cmd": "readExposome, loadExposome" }, { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": "Plots histograms of single or family of variables, plot results of applying a PCA to the set, plot the correlations computed across the variables, plot samples classification 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"language": [ "R" ], "license": "MIT", "collectionID": [ "BioConductor" ], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://bioconductor.org/packages/rexposome/", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/rexposome_1.20.0.tar.gz", "type": "Software package", "note": null, "version": "1.20.0" } ], "documentation": [ { "url": "http://bioconductor.org/packages/release/bioc/manuals/rexposome/man/rexposome.pdf", "type": [ "API documentation" ], "note": null }, { "url": "https://isglobal-brge.github.io/rexposome", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btz526", "pmid": "31243429", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Comprehensive study of the exposome and omic data using rexposome Bioconductor Packages", "abstract": "Summary: Genomics has dramatically improved our understanding of the molecular origins of certain human diseases. Nonetheless, our health is also influenced by the cumulative impact of exposures experienced across the life course (termed 'exposome'). The study of the high-dimensional exposome offers a new paradigm for investigating environmental contributions to disease etiology. However, there is a lack of bioinformatics tools for managing, visualizing and analyzing the exposome. The analysis data should include both association with health outcomes and integration with omic layers. We provide a generic framework called rexposome project, developed in the R/Bioconductor architecture that includes object-oriented classes and methods to leverage high-dimensional exposome data in disease association studies including its integration with a variety of high-throughput data types. The usefulness of the package is illustrated by analyzing a real dataset including exposome data, three health outcomes related to respiratory diseases and its integration with the transcriptome and methylome.", "date": "2019-12-15T00:00:00Z", "citationCount": 21, "authors": [ { "name": "Hernandez-Ferrer C." }, { "name": "Wellenius G.A." }, { "name": "Tamayo I." }, { "name": "Basagana X." }, { "name": "Sunyer J." }, { "name": "Vrijheid M." }, { "name": "Gonzalez J.R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1038/s41467-022-34422-2", "pmid": "36411288", "pmcid": "PMC9678903", "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Multi-omics signatures of the human early life exposome", "abstract": "Environmental exposures during early life play a critical role in life-course health, yet the molecular phenotypes underlying environmental effects on health are poorly understood. In the Human Early Life Exposome (HELIX) project, a multi-centre cohort of 1301 mother-child pairs, we associate individual exposomes consisting of >100 chemical, outdoor, social and lifestyle exposures assessed in pregnancy and childhood, with multi-omics profiles (methylome, transcriptome, proteins and metabolites) in childhood. We identify 1170 associations, 249 in pregnancy and 921 in childhood, which reveal potential biological responses and sources of exposure. Pregnancy exposures, including maternal smoking, cadmium and molybdenum, are predominantly associated with child DNA methylation changes. In contrast, childhood exposures are associated with features across all omics layers, most frequently the serum metabolome, revealing signatures for diet, toxic chemical compounds, essential trace elements, and weather conditions, among others. Our comprehensive and unique resource of all associations (https://helixomics.isglobal.org/) will serve to guide future investigation into the biological imprints of the early life exposome.", "date": "2022-12-01T00:00:00Z", "citationCount": 81, "authors": [ { "name": "Maitre L." }, { "name": "Bustamante M." }, { "name": "Hernandez-Ferrer C." }, { "name": "Thiel D." }, { "name": "Lau C.-H.E." }, { "name": "Siskos A.P." }, { "name": "Vives-Usano M." }, { "name": "Ruiz-Arenas C." }, { "name": "Pelegri-Siso D." }, { "name": "Robinson O." }, { "name": "Mason D." }, { "name": "Wright J." }, { "name": "Cadiou S." }, { "name": "Slama R." }, { "name": "Heude B." }, { "name": "Casas M." }, { "name": "Sunyer J." }, { "name": "Papadopoulou E.Z." }, { "name": "Gutzkow K.B." }, { "name": "Andrusaityte S." }, { "name": "Grazuleviciene R." }, { "name": "Vafeiadi M." }, { "name": "Chatzi L." }, { "name": "Sakhi A.K." }, { "name": "Thomsen C." }, { "name": "Tamayo I." }, { "name": "Nieuwenhuijsen M." }, { "name": "Urquiza J." }, { "name": "Borras E." }, { "name": "Sabido E." }, { "name": "Quintela I." }, { "name": "Carracedo A." }, { "name": "Estivill X." }, { "name": "Coen M." }, { "name": "Gonzalez J.R." }, { "name": "Keun H.C." }, { "name": "Vrijheid M." } ], "journal": "Nature Communications" } } ], "credit": [ { "name": "Carles Hernandez-Ferrer", "email": "carles.hernandez@isglobal.org", "url": "http://www.carleshf.com", "orcidid": "https://orcid.org/0000-0002-8029-7160", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Xavier Escribà Montagut", "email": "xavier.escriba@isglobal.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": "Juan R Gonzalez", "email": "juanr.gonzalez@isglobal.org", "url": "https://brge.isglobal.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "chernan3", "additionDate": "2018-07-25T15:26:58Z", "lastUpdate": "2025-05-29T11:42:05.422761Z", "editPermission": { "type": "group", "authors": [ "brgelab", "sergitobara", "chernan3" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "NestedComBat", "description": "This software performs feature-level harmonization of radiomic data extracted from medical images. Its primary goal is to reduce variability introduced by differences in acquisition protocols, scanner types, and imaging centers. The tool is based on the ComBat methodology, which uses an empirical Bayes linear model to correct batch effects by estimating location and scale parameters. It offers two harmonization strategies: the ComBat method, which aligns radiomic features to a common scale based on either all centers (ComBat) or a user-defined batch grouping (M-ComBat), and the Nested ComBat method, which enables simultaneous correction for multiple batch effects in hierarchical settings. 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It allows for the creation of personal identifiers (PID) from identifying attributes (IDAT), and thanks to the record linkage functionality, this is even possible with poor quality identifying data. The functions are available through a RESTful web interface.", "homepage": "https://bitbucket.org/medicalinformatics/mainzelliste/", "biotoolsID": "mainzelliste", "biotoolsCURIE": "biotools:mainzelliste", "version": [ "v1.13.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_4044", "term": "Data protection" }, { "uri": "http://edamontology.org/topic_3345", "term": "Data identity and mapping" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "AGPL-3.0", "collectionID": [ "EUCAIM", "eucaim", "Samply" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://helmholtz.software/software/mainzelliste", "type": [ "Software catalogue" ], "note": null }, { "url": "https://bitbucket.org/medicalinformatics/mainzelliste", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://bitbucket.org/medicalinformatics/mainzelliste/src/be269ba9466d022d6c691f9a78bd6e45f0abca8c/doc/getting-started.md", "type": [ "Installation instructions" ], "note": null } ], "publication": [ { "doi": "10.1186/s12911-014-0123-5", "pmid": "25656224", "pmcid": "PMC4350982", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "A RESTful interface to pseudonymization services in modern web applications", "abstract": "Background: Medical research networks rely on record linkage and pseudonymization to determine which records from different sources relate to the same patient. To establish informational separation of powers, the required identifying data are redirected to a trusted third party that has, in turn, no access to medical data. This pseudonymization service receives identifying data, compares them with a list of already reported patient records and replies with a (new or existing) pseudonym. We found existing solutions to be technically outdated, complex to implement or not suitable for internet-based research infrastructures. In this article, we propose a new RESTful pseudonymization interface tailored for use in web applications accessed by modern web browsers. Methods: The interface is modelled as a resource-oriented architecture, which is based on the representational state transfer (REST) architectural style. We translated typical use-cases into resources to be manipulated with well-known HTTP verbs. Patients can be re-identified in real-time by authorized users' web browsers using temporary identifiers. We encourage the use of PID strings for pseudonyms and the EpiLink algorithm for record linkage. As a proof of concept, we developed a Java Servlet as reference implementation. Results: The following resources have been identified: Sessions allow data associated with a client to be stored beyond a single request while still maintaining statelessness. Tokens authorize for a specified action and thus allow the delegation of authentication. Patients are identified by one or more pseudonyms and carry identifying fields. Relying on HTTP calls alone, the interface is firewall-friendly. The reference implementation has proven to be production stable. Conclusion: The RESTful pseudonymization interface fits the requirements of web-based scenarios and allows building applications that make pseudonymization transparent to the user using ordinary web technology. The open-source reference implementation implements the web interface as well as a scientifically grounded algorithm to generate non-speaking pseudonyms.", "date": "2015-02-07T00:00:00Z", "citationCount": 70, "authors": [ { "name": "Lablans M." }, { "name": "Borg A." }, { "name": "Uckert F." } ], "journal": "BMC Medical Informatics and Decision Making" } } ], "credit": [], "owner": "enola", "additionDate": "2025-05-22T17:46:59.585364Z", "lastUpdate": "2025-05-23T07:01:19.349987Z", "editPermission": { "type": "group", "authors": [ "tkussel" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Chevreul", "description": "An R package and shiny app for processing, plotting, and interactive exploratory data analysis of full-length scRNA-seq as SingleCellExperiments", "homepage": "https://cobriniklab.github.io/chevreul/", "biotoolsID": "chevreul", "biotoolsCURIE": "biotools:chevreul", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2945", "term": "Data analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3391", "term": "Omics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/cobriniklab/chevreul", "type": "Software package", "note": null, "version": "v1.0.0" } ], "documentation": [ { "url": "https://cobriniklab.github.io/chevreul/", "type": [ "Quick start guide" ], "note": null } ], "publication": [], "credit": [ { "name": "Kevin Stachelek", "email": "kevin.stachelek@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0003-2085-695X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "stachele", "additionDate": "2025-05-20T05:54:37.118800Z", "lastUpdate": "2025-05-20T05:56:27.709815Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }