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{ "count": 97, "next": "?page=2", "previous": null, "list": [ { "name": "bedtools_coveragebed_counts", "description": "Count the number of intervals in a BAM or BED file (the source) that overlap another BED file (the target).", "homepage": "https://github.com/arq5x/bedtools3", "biotoolsID": "bedtools_coveragebed_counts", "biotoolsCURIE": "biotools:bedtools_coveragebed_counts-ip", "version": [ "0.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_3003", "term": "BED" } ] }, { "data": { "uri": "http://edamontology.org/data_3002", "term": "Annotation track" }, "format": [ { "uri": "http://edamontology.org/format_3003", "term": "BED" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3002", "term": "Annotation track" }, "format": [ { "uri": "http://edamontology.org/format_3003", "term": "BED" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Shell", "Python" ], "license": null, "collectionID": [ "galaxyPasteur", "bedtools" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/bedtools_pasteur/bedtools_coveragebed_counts/0.1.0", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [ { "url": "http://quinlanlab.org/tutorials/bedtools/bedtools.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btq033", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "BEDTools: A flexible suite of utilities for comparing genomic features", "abstract": "Motivation: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing webbased methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner. Results: This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets. Availability and implementation: BEDTools was written in C++. Source code and a comprehensive user manual are freely available at http://code.google.com/p/bedtools. Contact: aaronquinlan@gmail.com; imh4y@virginia.edu. Supplementary information: Supplementary data are available at Bioinformatics online. © The Author(s) 2010. Published by Oxford University Press.", "date": "2010-01-28T00:00:00Z", "citationCount": 8825, "authors": [ { "name": "Quinlan A.R." }, { "name": "Hall I.M." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/nar/gkw343", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.High-throughput data production technologies, particularly 'next-generation' DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1025, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Von Kuster G." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic acids research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:29:58Z", "lastUpdate": "2022-06-01T04:14:29.977329Z", "editPermission": { "type": "group", "authors": [ "tcollins" ] }, "validated": 1, "homepage_status": 1, "elixir_badge": 0, "confidence_flag": null }, { "name": "sam_to_bam", "description": "Converts SAM format to BAM format.", "homepage": "http://www.htslib.org/", "biotoolsID": "sam_to_bam", "biotoolsCURIE": "biotools:sam_to_bam-ip", "version": [ "0.1.19" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" } ] }, { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C" ], "license": null, "collectionID": [ "galaxyPasteur", "SAMtools" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/samtobam/sam_to_bam/0.1.19", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [ { "url": "http://www.htslib.org/doc/samtools.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btp352", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "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": 24069, "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/nar/gkw343", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.High-throughput data production technologies, particularly 'next-generation' DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1022, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Von Kuster G." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic acids research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:26:14Z", "lastUpdate": "2020-08-16T18:32:41Z", "editPermission": { "type": "group", "authors": [ "alice" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "EOSC pipeline-Reproducibility", "description": "The described pipeline is aimed to replicate data stored at EGA generated by the GoNL consortium", "homepage": "https://github.com/CRG-CNAG/EOSC-Pilot", "biotoolsID": "eosc_pipeline-reproducibility", "biotoolsCURIE": "biotools:eosc_pipeline-reproducibility", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": "Human genome (hg19) fasta retrieval from bundle resource of GATK. Downloaded via command:\nwget -q ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/human_g1k_v37.fasta.gz", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3210", "term": "Genome index" }, "format": [ { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3210", "term": "Genome index" }, "format": [] } ], "note": "Human genome (hg19) fasta.fai retrieval from bundle resource of GATK. Downloaded via command:\nwget -q ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/human_g1k_v37.fasta.fai.gz", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3210", "term": "Genome index" }, "format": [ { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3210", "term": "Genome index" }, "format": [] } ], "note": "Human genome (hg19) fasta.dict retrieval from bundle resource of GATK. Downloaded via command:\nwget -q ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/human_g1k_v37.dict.gz", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "note": "dbSNP known variant retrieval from bundle resource of GATK. Downloaded via command:\nwget -q ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/dbsnp_138.b37.excluding_sites_after_129.vcf.gz", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "note": "1000Genomes Project known indels retrieval from bundle resource of GATK. Downloaded via command:\nwget -q ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.indels.b37.vcf.gz", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "note": "1000Genomes Project low coverage CEU genotypes retrieval from 1000Genomes Project repository. Downloaded via command:\nwget -q ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/release/2010_07/low_coverage/snps/CEU.low_coverage.2010_07.genotypes.vcf.gz", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3211", "term": "Genome indexing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3210", "term": "Genome index" }, "format": [] } ], "note": "Genome indexing obtained using bwa (version 0.5.8c). Used command:\nbwa index -a bwtsw human_g1k_v37.fasta", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3497", "term": "DNA sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0955", "term": "Data index" }, "format": [] } ], "note": "Input reads SA coordinates generation using bwa (version 0.5.8c). Used commands:\nbwa aln <genome fasta file> <fastq 1 file> -f \"prefix_1.sai\"\nbwa aln <genome fasta file> <fastq 2 file> -f \"prefix_2.sai\"", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3198", "term": "Read mapping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_0955", "term": "Data index" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0955", "term": "Data index" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3497", "term": "DNA sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_3497", "term": "DNA sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": "Read mapping obtained using bwa (version 0.5.8c) and picard tools (version 1.32). Used command:\nbwa sampe -P -p <platform> -i <lane> -m <sample ID> -l <library> <genome fasta file> <prefix_1.sai> <prefix_2.sai> <fastq 1 file> <fastq 2 file> | java -jar -Xmx4g picard-tools/SamFormatConverter.jar INPUT=/dev/stdin OUTPUT=<bam file>", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3802", "term": "Sorting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": "Mapped read sorting using picard tools (version 1.32) based on chromosome order on genome fasta file and coordinate position of mapped reads. Used command:\njava -jar -Xmx4g picard-tools/SortSam.jar INPUT=<bam file> OUTPUT=<sorted bam file> SORT_ORDER=coordinate", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0955", "term": "Data index" }, "format": [ { "uri": "http://edamontology.org/format_3327", "term": "BAI" } ] } ], "note": "Indexing of BAM sorted file using picard-tools (version 1.32). Used command:\njava -jar -Xmx4g picard-tools/BuildBamIndex.jar INPUT=<sorted bam file> OUTPUT=<sorted bam index file>", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": "Duplicated reads detection using picard-tools (version 1.32). Used command:\njava -jar -Xmx4g picard-tools/MarkDuplicates.jar INPUT=<sorted bam file> OUTPUT=<No duplicates bam file> METRICS_FILE=<metric file> REMOVE_DUPLICATES=false ASSUME_SORTED=true", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0955", "term": "Data index" }, "format": [ { "uri": "http://edamontology.org/format_3327", "term": "BAI" } ] } ], "note": "Indexing of BAM sorted file using picard-tools (version 1.32). Used command:\njava -jar -Xmx4g picard-tools/BuildBamIndex.jar INPUT=<No duplicates bam file> OUTPUT=<No duplicates bam index file>", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2089", "term": "Sequence alignment refinement" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2012", "term": "Sequence coordinates" }, "format": [ { "uri": "http://edamontology.org/format_3003", "term": "BED" } ] } ], "note": "Identification of suspicious intervals which are likely in need of realignment using GATK (version 1.1). Used command:\njava -Xmx10g -jar GenomeAnalysisTK.jar -l INFO -T RealignerTargetCreator -R <genome fasta file> -I <No duplicates bam file> -o <intervals file>", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2089", "term": "Sequence alignment refinement" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2012", "term": "Sequence coordinates" }, "format": [ { "uri": "http://edamontology.org/format_3003", "term": "BED" } ] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] }, { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": "Realignment around indels using GATK (version 1.1). Used command:\njava -Xmx10g -jar GenomeAnalysisTK.jar -l INFO -T IndelRealigner -U ALLOW_UNINDEXED_BAM -I <No duplicates bam file> -targetIntervals <intervals file> -R <genome fasta file> -known <dbsnp VCF file> -known <known indels 1000Genomes Project VCF file> -o <realigned bam file> -LOD 0.4 -compress 0", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2089", "term": "Sequence alignment refinement" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": "Fixing aligned mate pairs using picard tools (version 1.32). Used command:\njava -jar -Xmx4g picard-tools/FixMateInformation.jar INPUT=<realigned bam file> OUTPUT=<mate fixed bam SORT_ORDER=coordinate", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0955", "term": "Data index" }, "format": [ { "uri": "http://edamontology.org/format_3327", "term": "BAI" } ] } ], "note": "Indexing of BAM fixed mate file using picard-tools (version 1.32). Used command:\njava -jar -Xmx4g picard-tools/BuildBamIndex.jar INPUT=<mate fixed bam file> OUTPUT=<mate fixed bam index file>", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] }, { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": "Building model of covariation based on the data and a set of known variants retrieved from dbSNP and using GATK (version 1.1). Used command:\njava -jar -Xmx4g GenomeAnalysisTK.jar -l INFO -T CountCovariates -U ALLOW_UNINDEXED_BAM -R <genome fasta file> -knownSites <dbsnp VCF file> -I <mate fixed bam file> -cov ReadGroupcovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile <covariates csv table>", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2089", "term": "Sequence alignment refinement" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] }, { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": "Base recalibration based on model of covariation obtained in the previous step based on the data and a set of known variants using GATK (version 1.1). Used command:\njava -jar -Xmx4g GenomeAnalysisTK.jar -l INFO -T TableRecalibration -U ALLOW_UNINDEXED_BAM -R <genome fasta file> -I <mate fixed bam file> --recal_file <covariates csv table> --out <recalibrated bam>", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3802", "term": "Sorting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": "Recalibrated read sorting using picard tools (version 1.32) based on chromosome order on genome fasta file and coordinate position of mapped reads. Used command:\njava -jar -Xmx4g picard-tools/SortSam.jar INPUT=<recalibrated bam> OUTPUT=<sorted recalibrated bam> SORT_ORDER=coordinate", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0955", "term": "Data index" }, "format": [ { "uri": "http://edamontology.org/format_3327", "term": "BAI" } ] } ], "note": "java -jar -Xmx4g picard-tools/BuildBamIndex.jar INPUT=<sorted recalibrated bam> OUTPUT=<sorted recalibrated bam index file>", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] }, { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": "Building model of covariation based on the data and a set of known variants retrieved from dbSNP and using GATK (version 1.1). Used command:\njava -jar -Xmx4g GenomeAnalysisTK.jar -l INFO -T CountCovariates -U ALLOW_UNINDEXED_BAM -R <genome fasta file> -knownSites <dbsnp VCF file> -I <sorted recalibrated bam> -cov ReadGroupcovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile <recalibrated covariates csv table>", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] } ], "note": "Visualization of covariates computed before the base quality score recalibration using GATK (version 1.1) .Used command:\njava -jar -Xmx4g AnalyzeCovariates.jar -l INFO -resources <R path> --recal_file <mate fixed bam file> -outputDir <before folder>", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] } ], "note": "Visualization of covariates computed after the base quality score recalibration using GATK (version 1.1) .Used command:\njava -jar -Xmx4g AnalyzeCovariates.jar -l INFO -resources <R path> --recal_file <sorted recalibrated bam file> -outputDir <after folder>", "cmd": null } ], "toolType": [ "Workflow", "Command-line tool", "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Perl" ], "license": "Apache-1.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/CRG-CNAG/EOSC-Pilot", "type": "Source code", "note": "Repository of EOSC-Reproducibility pipeline", "version": null } ], "documentation": [], "publication": [], "credit": [ { "name": "Nino Spataro", "email": "nino.spataro@crg.eu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Paolo Di Tommaso", "email": "paolo.ditommaso@crg.eu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "spatariello", "additionDate": "2018-07-03T13:38:14Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "kWIP", "description": "The k-mer weighted inner product (kWIP) is a method for a de novo estimator of genetic similarity without the need of reference genome.", "homepage": "https://github.com/kdmurray91/kwip", "biotoolsID": "kwip", "biotoolsCURIE": "biotools:kwip", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" }, { "uri": "http://edamontology.org/operation_3731", "term": "Sample comparison" }, { "uri": "http://edamontology.org/operation_0289", "term": "Sequence distance matrix generation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0848", "term": "Raw sequence" }, "format": [ { "uri": "http://edamontology.org/format_2571", "term": "Raw sequence format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0870", "term": "Sequence distance matrix" }, "format": [ { "uri": "http://edamontology.org/format_3033", "term": "Matrix format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" } ], "operatingSystem": [], "language": [ "C++" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/kdmurray91/kWIP", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://kwip.readthedocs.io/en/latest/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1371/JOURNAL.PCBI.1005727", "pmid": "28873405", "pmcid": "PMC5600398", "type": [], "version": null, "note": null, "metadata": { "title": "kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity", "abstract": "© 2017 Murray et al.Modern genomics techniques generate overwhelming quantities of data. Extracting population genetic variation demands computationally efficient methods to determine genetic relatedness between individuals (or “samples”) in an unbiased manner, preferably de novo. Rapid estimation of genetic relatedness directly from sequencing data has the potential to overcome reference genome bias, and to verify that individuals belong to the correct genetic lineage before conclusions are drawn using mislabelled, or misidentified samples. We present the k-mer Weighted Inner Product (kWIP), an assembly-, and alignment-free estimator of genetic similarity. kWIP combines a probabilistic data structure with a novel metric, the weighted inner product (WIP), to efficiently calculate pairwise similarity between sequencing runs from their k-mer counts. It produces a distance matrix, which can then be further analysed and visualised. Our method does not require prior knowledge of the underlying genomes and applications include establishing sample identity and detecting mix-up, non-obvious genomic variation, and population structure. We show that kWIP can reconstruct the true relatedness between samples from simulated populations. By re-analysing several published datasets we show that our results are consistent with marker-based analyses. kWIP is written in C++, licensed under the GNU GPL, and is available from https://github.com/kdmurray91/kwip.", "date": "2017-09-01T00:00:00Z", "citationCount": 19, "authors": [ { "name": "Murray K.D." }, { "name": "Webers C." }, { "name": "Ong C.S." }, { "name": "Borevitz J." }, { "name": "Warthmann N." } ], "journal": "PLoS Computational Biology" } } ], "credit": [ { "name": "Kevin Murray", "email": null, "url": "https://github.com/kdmurray91", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "d.gabrielaitis", "additionDate": "2018-04-29T10:44:43Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PCSF", "description": "R-Package for network-based interpretation of high-throughput data.", "homepage": "https://github.com/IOR-Bioinformatics/PCSF", "biotoolsID": "pcsf", "biotoolsCURIE": "biotools:pcsf", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3439", "term": "Pathway or network prediction" }, { "uri": "http://edamontology.org/operation_2464", "term": "Protein-protein interaction prediction" }, { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2600", "term": "Pathway or network" }, "format": [ { "uri": "http://edamontology.org/format_3617", "term": "Graph format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2600", "term": "Pathway or network" }, "format": [ { "uri": "http://edamontology.org/format_3617", "term": "Graph format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_1775", "term": "Function analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R", "C++" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/IOR-Bioinformatics/PCSF", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/IOR-Bioinformatics/PCSF/tree/master/vignettes", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pcbi.1005694", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PCSF: An R-package for network-based interpretation of high-throughput data", "abstract": "© 2017 Akhmedov et al.With the recent technological developments a vast amount of high-throughput data has been profiled to understand the mechanism of complex diseases. The current bioinformatics challenge is to interpret the data and underlying biology, where efficient algorithms for analyzing heterogeneous high-throughput data using biological networks are becoming increasingly valuable. In this paper, we propose a software package based on the Prize-collecting Steiner Forest graph optimization approach. The PCSF package performs fast and user-friendly network analysis of high-throughput data by mapping the data onto a biological networks such as protein-protein interaction, gene-gene interaction or any other correlation or coexpression based networks. Using the interaction networks as a template, it determines high-confidence subnetworks relevant to the data, which potentially leads to predictions of functional units. It also interactively visualizes the resulting subnetwork with functional enrichment analysis.", "date": "2017-07-01T00:00:00Z", "citationCount": 11, "authors": [ { "name": "Akhmedov M." }, { "name": "Kedaigle A." }, { "name": "Chong R.E." }, { "name": "Montemanni R." }, { "name": "Bertoni F." }, { "name": "Fraenkel E." }, { "name": "Kwee I." } ], "journal": "PLoS Computational Biology" } } ], "credit": [ { "name": "Murodzhon Akhmedov", "email": "murodzhon@idsia.ch", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "migle_sur", "additionDate": "2018-06-20T16:01:50Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Mendel,MD", "description": "Online tool created to help doctors and scientists to identify disease causing variants in human exome/genome sequencing data from patients with Mendelian disorders.", "homepage": "https://mendelmd.org/", "biotoolsID": "mendelmd", "biotoolsCURIE": "biotools:mendelmd", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3695", "term": "Filtering" }, { "uri": "http://edamontology.org/operation_3672", "term": "Gene functional annotation" }, { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_1775", "term": "Function analysis" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" }, { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://mendelmd.readthedocs.io/en/latest/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pcbi.1005520", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Mendel,MD: A user-friendly open-source web tool for analyzing WES and WGS in the diagnosis of patients with Mendelian disorders", "abstract": "© 2017 G. C. C. L. Cardenas et al.Whole exome and whole genome sequencing have both become widely adopted methods for investigating and diagnosing human Mendelian disorders. As pangenomic agnostic tests, they are capable of more accurate and agile diagnosis compared to traditional sequencing methods. This article describes new software called Mendel,MD, which combines multiple types of filter options and makes use of regularly updated databases to facilitate exome and genome annotation, the filtering process and the selection of candidate genes and variants for experimental validation and possible diagnosis. This tool offers a user-friendly interface, and leads clinicians through simple steps by limiting the number of candidates to achieve a final diagnosis of a medical genetics case. A useful innovation is the “1-click” method, which enables listing all the relevant variants in genes present at OMIM for perusal by clinicians. Mendel,MD was experimentally validated using clinical cases from the literature and was tested by students at the Universidade Federal de Minas Gerais, at GENE–Núcleo de Genética Médica in Brazil and at the Children’s University Hospital in Dublin, Ireland. We show in this article how it can simplify and increase the speed of identifying the culprit mutation in each of the clinical cases that were received for further investigation. Mendel,MD proved to be a reliable web-based tool, being open-source and time efficient for identifying the culprit mutation in different clinical cases of patients with Mendelian Disorders. It is also freely accessible for academic users on the following URL: https://mendelmd.org.", "date": "2017-06-01T00:00:00Z", "citationCount": 3, "authors": [ { "name": "G. C. C. L. Cardenas R." }, { "name": "D. Linhares N." }, { "name": "L. Ferreira R." }, { "name": "Pena S.D.J." } ], "journal": "PLoS Computational Biology" } } ], "credit": [ { "name": "Sérgio D. J. Pena", "email": "spena@dcc.ufmg.br", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "migle_sur", "additionDate": "2018-06-19T19:52:08Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ITSxpress", "description": "ITSxpress: Software to rapidly trim the Internally transcribed spacer (ITS) region of FASTQ files", "homepage": "https://github.com/USDA-ARS-GBRU/itsxpress", "biotoolsID": "itsxpress", "biotoolsCURIE": "biotools:itsxpress", "version": [ "v1.6.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2975", "term": "Nucleic acid sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_2182", "term": "FASTQ-like format (text)" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2975", "term": "Nucleic acid sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_2545", "term": "FASTQ-like format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python" ], "license": "CC0-1.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/USDA-ARS-GBRU/itsxpress", "type": [ "Repository" ], "note": null }, { "url": "https://pypi.org/project/itsxpress/", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Adam Rivers", "email": "adam.rivers@ars.usda.gov", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": "Adam Rivers", "email": null, "url": "https://tinyecology.com", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "arivers", "additionDate": "2018-07-03T14:53:16Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "q2_ITSxpress", "description": "q2_ITSxpress: a Qiime2 plugin for ITSxpress, software to rapidly trim the Internally transcribed spacer (ITS) region of FASTQ files", "homepage": "https://github.com/USDA-ARS-GBRU/q2_itsxpress", "biotoolsID": "q2_itsxpress", "biotoolsCURIE": "biotools:q2_itsxpress", "version": [ "v1.6.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2975", "term": "Nucleic acid sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_2182", "term": "FASTQ-like format (text)" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2975", "term": "Nucleic acid sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_2182", "term": "FASTQ-like format (text)" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python" ], "license": "CC0-1.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/USDA-ARS-GBRU/q2_itsxpress", "type": [ "Repository" ], "note": null }, { "url": "https://pypi.org/project/q2_itsxpress/", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Adam Rivers", "email": "adam.rivers@ars.usda.gov", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Kyle Weber", "email": "kweber1@uf.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Adam Rivers", "email": null, "url": "https://tinyecology.com", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "arivers", "additionDate": "2018-07-13T20:26:51Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "NetControl4BioMed", "description": "The pipeline can be used by researchers for controlling and better understanding of molecular interaction networks through combinatorial multi-drug therapies, for more efficient therapeutic approaches and personalised medicine.", "homepage": "http://combio.abo.fi/research/network-controlability-project/", "biotoolsID": "netcontrol4biomed", "biotoolsCURIE": "biotools:netcontrol4biomed", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2464", "term": "Protein-protein interaction prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Cancer" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "PHP", "Python" ], "license": "BSD-2-Clause-FreeBSD", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://combio.abo.fi/nc/net_control/remote_call.php", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "http://combio.abo.fi/scm/git/netcontrol", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://combio.abo.fi/nc/net_control/documentation.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-018-2177-3", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "NetControl4BioMed: A pipeline for biomedical data acquisition and analysis of network controllability", "abstract": "© 2018 The Author(s).Background: Network controllability focuses on discovering combinations of external interventions that can drive a biological system to a desired configuration. In practice, this approach translates into finding a combined multi-drug therapy in order to induce a desired response from a cell; this can lead to developments of novel therapeutic approaches for systemic diseases like cancer. Result: We develop a novel bioinformatics data analysis pipeline called NetControl4BioMed based on the concept of target structural control of linear networks. Our pipeline generates novel molecular interaction networks by combining pathway data from various public databases starting from the user's query. The pipeline then identifies a set of nodes that is enough to control a given, user-defined set of disease-specific essential proteins in the network, i.e., it is able to induce a change in their configuration from any initial state to any final state. We provide both the source code of the pipeline as well as an online web-service based on this pipeline http://combio.abo.fi/nc/net_control/remote_call.php. Conclusion: The pipeline can be used by researchers for controlling and better understanding of molecular interaction networks through combinatorial multi-drug therapies, for more efficient therapeutic approaches and personalised medicine.", "date": "2018-07-09T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Kanhaiya K." }, { "name": "Rogojin V." }, { "name": "Kazemi K." }, { "name": "Czeizler E." }, { "name": "Petre I." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Ion Petre", "email": "ipetre@abo.fi", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "shadi.m", "additionDate": "2018-07-29T11:25:53Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FC_analysis", "description": "This open source software package automatically analyses single force curves or entire force volume maps to yield the corresponding elasticity and deformability images. The principal characteristic of the package is a large adaptability to the various experimental setups and to different analysis methodologies.", "homepage": "http://uk.mathworks.com/products/compiler/mcr", "biotoolsID": "fc_analysis", "biotoolsCURIE": "biotools:fc_analysis", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2945", "term": "Analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Plug-in" ], "topic": [ { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Windows" ], "language": [ "MATLAB" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://static-content.springer.com/esm/art%3A10.1186%2Fs12859-018-2265-4/MediaObjects/12859_2018_2265_MOESM1_ESM.exe", "type": "Software package", "note": null, "version": null } ], "documentation": [], "publication": [ { "doi": "10.1186/s12859-018-2265-4", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "FC_analysis: A tool for investigating atomic force microscopy maps of force curves", "abstract": "© 2018 The Author(s).Background: The collection and analysis of Atomic Force Microscopy force curves is a well-established procedure to obtain high-resolution information of non-topographic data from any kind of sample, including biological specimens. In particular, these analyses are commonly employed to study elasticity, stiffness or adhesion properties of the samples. Furthermore, the collection of several force curves over an extended area of the specimens allows reconstructing maps, called force volume maps, of the spatial distribution of the mechanical properties. Coupling these maps with the conventional high-resolution topographic reconstruction of the sample's surface, provides a deeper insight on the sample composition from the structural and nanomechanical point of view. Results: In this paper we present the open source software package FC_analysis that automatically analyses single force curves or entire force volume maps to yield the corresponding elasticity and deformability images. The principal characteristic of the FC_analysis is a large adaptability to the various experimental setups and to different analysis methodologies. For instance, the user can provide custom values for the detector sensitivity, scanner-z sensitivity, cantilever's elastic constant and map's acquisition modality and can choose between different analysis methodologies. Furthermore, the software allows the optimization of the fitting parameters and gives direct control on each step of the analysis procedure. Notably, to overcome a limitation common to many other analysis programs, FC_analysis can be applied to a rectangular portion of the image, allowing the analysis of inhomogeneous samples. Finally, the software allows reconstructing a Young's modulus map at different penetration depths, enabling the use of modern investigation tools such as the force tomography. Conclusions: The FC_analysis software aims to become a useful tool for the analysis of force curves maps collected using custom or commercial Atomic Force Microscopes, and is especially useful in those cases for which the producer doesn't release a dedicated software.", "date": "2018-07-06T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Dinarelli S." }, { "name": "Girasole M." }, { "name": "Longo G." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Simone Dinarelli", "email": "simone.dinarelli@ism.cnr.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "shadi.m", "additionDate": "2018-07-29T11:54:35Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PepBonPred", "description": "PepBindPred is for users interested in identifying peptide binding regions within a protein sequence, which may bind to a know protein structure. PepBindPred was trained on a set of non-redundant protein sequences containing known peptide binding regions sourced from the ELM database.", "homepage": "http://bioware.ucd.ie/~compass/biowareweb/Server_pages/pepbindpred.php", "biotoolsID": "pepbonpred", "biotoolsCURIE": "biotools:pepbonpred", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2258", "term": "Cheminformatics" }, { "uri": "http://edamontology.org/topic_1317", "term": "Structural biology" }, { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" }, { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Perl" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://bioware.ucd.ie/~compass/biowareweb/Server_pages/pepbindpred.php", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [ { "url": "http://bioware.ucd.ie/~compass/biowareweb/Server_pages/pepbindpred.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pone.0072838", "pmid": "24019881", "pmcid": "PMC3760854", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Predicting Binding within Disordered Protein Regions to Structurally Characterised Peptide-Binding Domains", "abstract": "Disordered regions of proteins often bind to structured domains, mediating interactions within and between proteins. However, it is difficult to identify a priori the short disordered regions involved in binding. We set out to determine if docking such peptide regions to peptide binding domains would assist in these predictions.We assembled a redundancy reduced dataset of SLiM (Short Linear Motif) containing proteins from the ELM database. We selected 84 sequences which had an associated PDB structures showing the SLiM bound to a protein receptor, where the SLiM was found within a 50 residue region of the protein sequence which was predicted to be disordered. First, we investigated the Vina docking scores of overlapping tripeptides from the 50 residue SLiM containing disordered regions of the protein sequence to the corresponding PDB domain. We found only weak discrimination of docking scores between peptides involved in binding and adjacent non-binding peptides in this context (AUC 0.58).Next, we trained a bidirectional recurrent neural network (BRNN) using as input the protein sequence, predicted secondary structure, Vina docking score and predicted disorder score. The results were very promising (AUC 0.72) showing that multiple sources of information can be combined to produce results which are clearly superior to any single source.We conclude that the Vina docking score alone has only modest power to define the location of a peptide within a larger protein region known to contain it. However, combining this information with other knowledge (using machine learning methods) clearly improves the identification of peptide binding regions within a protein sequence. This approach combining docking with machine learning is primarily a predictor of binding to peptide-binding sites, and is not intended as a predictor of specificity of binding to particular receptors. © 2013 Khan et al.", "date": "2013-09-03T00:00:00Z", "citationCount": 21, "authors": [ { "name": "Khan W." }, { "name": "Duffy F." }, { "name": "Pollastri G." }, { "name": "Shields D.C." }, { "name": "Mooney C." } ], "journal": "PLoS ONE" } } ], "credit": [ { "name": "Prof. Dr. Denis C. Shields", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": null, "email": "waqasnayab@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "WaqasuddinKhan", "additionDate": "2018-08-02T10:04:31Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PepBindPred", "description": "PepBindPred is for users interested in identifying peptide binding regions within a protein sequence, which may bind to a know protein structure. PepBindPred was trained on a set of non-redundant protein sequences containing known peptide binding regions sourced from the ELM database.", "homepage": "http://bioware.ucd.ie/~compass/biowareweb/Server_pages/pepbindpred.php", "biotoolsID": "pepbindpred", "biotoolsCURIE": "biotools:pepbindpred", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2258", "term": "Cheminformatics" }, { "uri": "http://edamontology.org/topic_1317", "term": "Structural biology" }, { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" }, { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Perl" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://bioware.ucd.ie/~compass/biowareweb/Server_pages/pepbindpred.php", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [ { "url": "http://bioware.ucd.ie/~compass/biowareweb/Server_pages/pepbindpred.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pone.0072838", "pmid": "24019881", "pmcid": "PMC3760854", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Predicting Binding within Disordered Protein Regions to Structurally Characterised Peptide-Binding Domains", "abstract": "Disordered regions of proteins often bind to structured domains, mediating interactions within and between proteins. However, it is difficult to identify a priori the short disordered regions involved in binding. We set out to determine if docking such peptide regions to peptide binding domains would assist in these predictions.We assembled a redundancy reduced dataset of SLiM (Short Linear Motif) containing proteins from the ELM database. We selected 84 sequences which had an associated PDB structures showing the SLiM bound to a protein receptor, where the SLiM was found within a 50 residue region of the protein sequence which was predicted to be disordered. First, we investigated the Vina docking scores of overlapping tripeptides from the 50 residue SLiM containing disordered regions of the protein sequence to the corresponding PDB domain. We found only weak discrimination of docking scores between peptides involved in binding and adjacent non-binding peptides in this context (AUC 0.58).Next, we trained a bidirectional recurrent neural network (BRNN) using as input the protein sequence, predicted secondary structure, Vina docking score and predicted disorder score. The results were very promising (AUC 0.72) showing that multiple sources of information can be combined to produce results which are clearly superior to any single source.We conclude that the Vina docking score alone has only modest power to define the location of a peptide within a larger protein region known to contain it. However, combining this information with other knowledge (using machine learning methods) clearly improves the identification of peptide binding regions within a protein sequence. This approach combining docking with machine learning is primarily a predictor of binding to peptide-binding sites, and is not intended as a predictor of specificity of binding to particular receptors. © 2013 Khan et al.", "date": "2013-09-03T00:00:00Z", "citationCount": 21, "authors": [ { "name": "Khan W." }, { "name": "Duffy F." }, { "name": "Pollastri G." }, { "name": "Shields D.C." }, { "name": "Mooney C." } ], "journal": "PLoS ONE" } } ], "credit": [ { "name": "Prof. Dr. Denis C. Shields", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": null, "email": "waqasnayab@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "WaqasuddinKhan", "additionDate": "2018-08-02T10:05:27Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MEGADOCK-Web", "description": "It is an integrated database of high-throughput structure-based PPI predictions.", "homepage": "http://www.bi.cs.titech.ac.jp/megadock-web/", "biotoolsID": "megadock-web", "biotoolsCURIE": "biotools:megadock-web", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2464", "term": "Protein-protein interaction prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s12859-018-2073-x", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "MEGADOCK-Web: An integrated database of high-throughput structure-based protein-protein interaction predictions", "abstract": "© 2018 The Author(s).Background: Protein-protein interactions (PPIs) play several roles in living cells, and computational PPI prediction is a major focus of many researchers. The three-dimensional (3D) structure and binding surface are important for the design of PPI inhibitors. Therefore, rigid body protein-protein docking calculations for two protein structures are expected to allow elucidation of PPIs different from known complexes in terms of 3D structures because known PPI information is not explicitly required. We have developed rapid PPI prediction software based on protein-protein docking, called MEGADOCK. In order to fully utilize the benefits of computational PPI predictions, it is necessary to construct a comprehensive database to gather prediction results and their predicted 3D complex structures and to make them easily accessible. Although several databases exist that provide predicted PPIs, the previous databases do not contain a sufficient number of entries for the purpose of discovering novel PPIs. Results: In this study, we constructed an integrated database of MEGADOCK PPI predictions, named MEGADOCK-Web. MEGADOCK-Web provides more than 10 times the number of PPI predictions than previous databases and enables users to conduct PPI predictions that cannot be found in conventional PPI prediction databases. In MEGADOCK-Web, there are 7528 protein chains and 28,331,628 predicted PPIs from all possible combinations of those proteins. Each protein structure is annotated with PDB ID, chain ID, UniProt AC, related KEGG pathway IDs, and known PPI pairs. Additionally, MEGADOCK-Web provides four powerful functions: 1) searching precalculated PPI predictions, 2) providing annotations for each predicted protein pair with an experimentally known PPI, 3) visualizing candidates that may interact with the query protein on biochemical pathways, and 4) visualizing predicted complex structures through a 3D molecular viewer. Conclusion: MEGADOCK-Web provides a huge amount of comprehensive PPI predictions based on docking calculations with biochemical pathways and enables users to easily and quickly assess PPI feasibilities by archiving PPI predictions. MEGADOCK-Web also promotes the discovery of new PPIs and protein functions and is freely available for use at http://www.bi.cs.titech.ac.jp/megadock-web/.", "date": "2018-05-08T00:00:00Z", "citationCount": 8, "authors": [ { "name": "Hayashi T." }, { "name": "Matsuzaki Y." }, { "name": "Yanagisawa K." }, { "name": "Ohue M." }, { "name": "Akiyama Y." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Masahito Ohue", "email": "ohue@c.titech.ac.jp", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Yutaka Akiyama", "email": "akiyama@c.titech.ac.jp", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "shadi.m", "additionDate": "2018-08-06T13:08:41Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BIP", "description": "Brassica Information Portal.", "homepage": "https://bip.earlham.ac.uk/", "biotoolsID": "bip", "biotoolsCURIE": "biotools:bip", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_3695", "term": "Filtering" }, { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" }, { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] } ], "output": [], "note": "crop phenotyping data", "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3298", "term": "Phenomics" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Ruby" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/TGAC/brassica", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://bip.earlham.ac.uk/api_documentation", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.12688/f1000research.11301.1", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data", "abstract": "© 2017 Eckes AH et al.The Brassica Information Portal (BIP) is a centralised repository for Brassica phenotypic data. Trait data associated with Brassica research and breeding experiments conducted on Brassica crops, used as vegetables, for livestock fodder and biofuels, is hosted on the site, together with information on the experimental plant materials used, as well as trial design. BIP is an open access and open source project, built on the schema of CropStoreDB, and as such can provide trait data management strategies for any crop data. A new user interface and programmatic submission/retrieval system helps to simplify data access for scientists and breeders. BIP opens up the opportunity to apply big data analyses to data generated by the Brassica Research Community. Here, we present a short description of the current status of the repository.", "date": "2017-01-01T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Jurkowski W." }, { "name": "Eckes A.H." }, { "name": "Gubala T." }, { "name": "Nowakowski P." }, { "name": "Szymczyszyn T." }, { "name": "Wells R." }, { "name": "Irwin J.A." }, { "name": "Horro C." }, { "name": "Hancock J.M." }, { "name": "King G." }, { "name": "Dyer S.C." } ], "journal": "F1000Research" } } ], "credit": [ { "name": null, "email": "bip@earlham.ac.uk", "url": "https://bip.earlham.ac.uk", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": null, "email": "wiktor.jurkowski@earlham.ac.uk", "url": "http://www.earlham.ac.uk/jurkowski-group", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "wjurki", "additionDate": "2017-02-02T14:45:59Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FGMP", "description": "Genome completeness assessment tool focused on Fungi", "homepage": "http://github.com/stajichlab/FGMP", "biotoolsID": "fgmp", "biotoolsCURIE": "biotools:fgmp", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3180", "term": "Sequence assembly validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0925", "term": "Sequence assembly" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3181", "term": "Sequence assembly report" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" }, { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_0097", "term": "Nucleic acid structure analysis" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Perl" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/stajichlab/FGMP", "type": [ "Repository" ], "note": "Github repository (main site)" } ], "download": [ { "url": "https://github.com/stajichlab/FGMP/releases", "type": "Source code", "note": "Latest release code available from this URL", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1101/049619", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Ousmane Cissé", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, 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"https://github.com/bioexcel/virtualscreening", "biotoolsID": "virtualscreening", "biotoolsCURIE": "biotools:virtualscreening", "version": [ "Alpha" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2423", "term": "Prediction and recognition" }, { "uri": "http://edamontology.org/operation_2425", "term": "Optimisation and refinement" }, { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_0883", "term": "Structure" }, "format": [ { "uri": "http://edamontology.org/format_3816", "term": "Mol2" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_3314", "term": "Chemistry" }, { "uri": "http://edamontology.org/topic_3344", "term": "Biomedical science" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "BioExcel" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/bioexcel/virtualscreening", "type": [ "Repository" ], "note": "VirtualScreening is a Python package inheriting from pymdsetup to perform virtual screening on a set of predefined targets" } ], "download": [ { "url": "https://github.com/bioexcel/virtualscreening", "type": "Source code", "note": "VirtualScreening is a Python package inheriting from pymdsetup to perform virtual screening on a set of predefined targets", "version": null } ], "documentation": [ { "url": "https://github.com/bioexcel/virtualscreening/blob/master/README.md", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.5281/zenodo.263965", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "BioExcel Center of Excellence for Computational Biomolecular Research", "email": null, "url": "https://bioexcel.eu", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Pau Andrio", "email": "pau.andrio@bsc.es", "url": "https://github.com/bioexcel/virtualscreening", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "adam.hospital@irbbarcelona.org", "additionDate": "2018-10-18T14:31:58Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "group", "authors": [ "gelpi@ub.edu" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DISEASES", "description": "DISEASES is a weekly updated web resource that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. We further unify the evidence by assigning confidence scores that facilitate comparison of the different types and sources of evidence.", "homepage": "https://diseases.jensenlab.org/", "biotoolsID": "diseases", "biotoolsCURIE": "biotools:diseases", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1025", "term": "Gene identifier" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3667", "term": "Disease identifier" }, "format": [] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3667", "term": "Disease identifier" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1025", "term": "Gene identifier" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0218", "term": "Natural language processing" }, { "uri": "http://edamontology.org/topic_3517", "term": "GWAS study" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC-BY-4.0", "collectionID": [ "JensenLab" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://diseases.jensenlab.org/Downloads", "type": "Biological data", "note": "Bulk download files in tab-delimited format.", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1016/j.ymeth.2014.11.020", "pmid": "25484339", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "DISEASES: Text mining and data integration of disease-gene associations", "abstract": "© 2014 The Authors.Text mining is a flexible technology that can be applied to numerous different tasks in biology and medicine. We present a system for extracting disease-gene associations from biomedical abstracts. The system consists of a highly efficient dictionary-based tagger for named entity recognition of human genes and diseases, which we combine with a scoring scheme that takes into account co-occurrences both within and between sentences. We show that this approach is able to extract half of all manually curated associations with a false positive rate of only 0.16%. Nonetheless, text mining should not stand alone, but be combined with other types of evidence. For this reason, we have developed the DISEASES resource, which integrates the results from text mining with manually curated disease-gene associations, cancer mutation data, and genome-wide association studies from existing databases. The DISEASES resource is accessible through a web interface at http://diseases.jensenlab.org/, where the text-mining software and all associations are also freely available for download.", "date": "2015-03-01T00:00:00Z", "citationCount": 248, "authors": [ { "name": "Pletscher-Frankild S." }, { "name": "Palleja A." }, { "name": "Tsafou K." }, { "name": "Binder J.X." }, { "name": "Jensen L.J." } ], "journal": "Methods" } } ], "credit": [ { "name": "Lars Juhl Jensen", "email": "lars.juhl.jensen@cpr.ku.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "larsjuhljensen", "additionDate": "2018-02-23T09:36:20Z", "lastUpdate": "2020-06-16T10:55:20Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "COMPARTMENTS", "description": "COMPARTMENTS is a weekly updated web resource that integrates evidence on protein subcellular localization from manually curated literature, high-throughput screens, automatic text mining, and sequence-based prediction methods. We map all evidence to common protein identifiers and Gene Ontology terms, and further unify it by assigning confidence scores that facilitate comparison of the different types and sources of evidence and visualize these scores on a schematic cell.", "homepage": "https://compartments.jensenlab.org/", "biotoolsID": "compartments", "biotoolsCURIE": "biotools:compartments", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1025", "term": "Gene identifier" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1176", "term": "GO concept ID" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0140", "term": "Protein targeting and localisation" }, { "uri": "http://edamontology.org/topic_0218", "term": "Natural language processing" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC-BY-4.0", "collectionID": [ "JensenLab" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://compartments.jensenlab.org/Downloads", "type": "Biological data", "note": "Bulk download files in tab-delimited format.", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1093/database/bau012", "pmid": "24573882", "pmcid": "PMC3935310", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "COMPARTMENTS: Unification and visualization of protein subcellular localization evidence", "abstract": "© The Author(s) 2014.Information on protein subcellular localization is important to understand the cellular functions of proteins. Currently, such information is manually curated from the literature, obtained from high-throughput microscopy-based screens and predicted from primary sequence. To get a comprehensive view of the localization of a protein, it is thus necessary to consult multiple databases and prediction tools. To address this, we present the COMPARTMENTS resource, which integrates all sources listed above as well as the results of automatic text mining. The resource is automatically kept up to date with source databases, and all localization evidence is mapped onto common protein identifiers and Gene Ontology terms. We further assign confidence scores to the localization evidence to facilitate comparison of different types and sources of evidence. To further improve the comparability, we assign confidence scores based on the type and source of the localization evidence. Finally, we visualize the unified localization evidence for a protein on a schematic cell to provide a simple overview.", "date": "2014-01-01T00:00:00Z", "citationCount": 221, "authors": [ { "name": "Binder J.X." }, { "name": "Pletscher-Frankild S." }, { "name": "Tsafou K." }, { "name": "Stolte C." }, { "name": "O'Donoghue S.I." }, { "name": "Schneider R." }, { "name": "Jensen L.J." } ], "journal": "Database" } } ], "credit": [ { "name": "Lars Juhl Jensen", "email": "lars.juhl.jensen@cpr.ku.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "larsjuhljensen", "additionDate": "2018-02-23T10:16:53Z", "lastUpdate": "2020-06-16T10:55:20Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ORGANISMS", "description": "ORGANISMS is a weekly updated web resource that facilitates taxonomy-aware search and retrieval of articles. To this end, the the resource performs named entity recognition of terms from the NCBI Taxonomy on PubMed abstracts. The resource further provides download files of organism-disease and organism-tissue associations extracted through automatic text mining.", "homepage": "https://organisms.jensenlab.org/", "biotoolsID": "organisms", "biotoolsCURIE": "biotools:organisms", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0305", "term": "Literature search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1869", "term": "Organism identifier" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1187", "term": "PubMed ID" }, "format": [ { "uri": "http://edamontology.org/format_2020", "term": "Article format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0218", "term": "Natural language processing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC-BY-4.0", "collectionID": [ "JensenLab" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://organisms.jensenlab.org/Downloads", "type": "Biological data", "note": "Bulk download files in tab-delimited format.", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1371/journal.pone.0065390", "pmid": "23823062", "pmcid": "PMC3688812", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text", "abstract": "The exponential growth of the biomedical literature is making the need for efficient, accurate text-mining tools increasingly clear. The identification of named biological entities in text is a central and difficult task. We have developed an efficient algorithm and implementation of a dictionary-based approach to named entity recognition, which we here use to identify names of species and other taxa in text. The tool, SPECIES, is more than an order of magnitude faster and as accurate as existing tools. The precision and recall was assessed both on an existing gold-standard corpus and on a new corpus of 800 abstracts, which were manually annotated after the development of the tool. The corpus comprises abstracts from journals selected to represent many taxonomic groups, which gives insights into which types of organism names are hard to detect and which are easy. Finally, we have tagged organism names in the entire Medline database and developed a web resource, ORGANISMS, that makes the results accessible to the broad community of biologists. The SPECIES software is open source and can be downloaded from http://species.jensenlab.org along with dictionary files and the manually annotated gold-standard corpus. The ORGANISMS web resource can be found at http://organisms.jensenlab.org. © 2013 Pafilis et al.", "date": "2013-06-18T00:00:00Z", "citationCount": 55, "authors": [ { "name": "Pafilis E." }, { "name": "Frankild S.P." }, { "name": "Fanini L." }, { "name": "Faulwetter S." }, { "name": "Pavloudi C." }, { "name": "Vasileiadou A." }, { "name": "Arvanitidis C." }, { "name": "Jensen L.J." } ], "journal": "PLoS ONE" } } ], "credit": [ { "name": "Lars Juhl Jensen", "email": "lars.juhl.jensen@cpr.ku.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "larsjuhljensen", "additionDate": "2018-02-25T10:17:45Z", "lastUpdate": "2020-06-16T10:55:20Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "TriFusion", "description": "Modern GUI and command line application designed to make the life of anyone with proteome and/or alignment sequence data easier and more pleasurable. It allows user to process their data through three independent modules: (i) Search and explore orthologs across multiple proteomes; (ii) Convert, concatenate, collapse, filter and perform many other manipulations of thousands sequence alignments files. 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Large scale metagenomic projects aim to extract biodiversity knowledge between different environmental conditions. Current methods for comparing microbial communities face important limitations. Those based on taxonomical or functional assignation rely on a small subset of the sequences that can be associated to known organisms. On the other hand, de novo methods, that compare the whole sets of sequences, either do not scale up on ambitious metagenomic projects or do not provide precise and exhaustive results. Methods. These limitations motivated the development of a new de novo metagenomic comparative method, called Simka. This method computes a large collection of standard ecological distances by replacing species counts by k-mer counts. Simka scales-up today's metagenomic projects thanks to a new parallel k-mer counting strategy on multiple datasets. Results. Experiments on public Human Microbiome Project datasets demonstrate that Simka captures the essential underlying biological structure. Simka was able to compute in a few hours both qualitative and quantitative ecological distances on hundreds of metagenomic samples (690 samples, 32 billions of reads). 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Published by Oxford University Press on behalf of Nucleic Acids Research.High-throughput data production technologies, particularly 'next-generation' DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. 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Published by Oxford University Press on behalf of Nucleic Acids Research.High-throughput data production technologies, particularly 'next-generation' DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1025, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Von Kuster G." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic acids research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:23:42Z", "lastUpdate": "2020-06-16T10:55:20Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "gdtools_gd2vcf", "description": "Creates a Variant Call Format (VCF) file of mutations present in an input Genome Diff file.", "homepage": "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html", "biotoolsID": "gdtools_gd2vcf", "biotoolsCURIE": "biotools:gdtools_gd2vcf-ip", "version": [ "0.26" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "galaxyPasteur", "gdtools" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/mvalade/gdtools/gdtools_GD2VCF/0.26", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [ { "url": "https://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr%2Frepos%2Fmvalade%2Fgdtools%2Fgdtools_GD2VCF%2F0.26", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/1471-2164-15-1039", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq", "abstract": "© 2014 Barrick et al.Background: Mutations that alter chromosomal structure play critical roles in evolution and disease, including in the origin of new lifestyles and pathogenic traits in microbes. Large-scale rearrangements in genomes are often mediated by recombination events involving new or existing copies of mobile genetic elements, recently duplicated genes, or other repetitive sequences. Most current software programs for predicting structural variation from short-read DNA resequencing data are intended primarily for use on human genomes. They typically disregard information in reads mapping to repeat sequences, and significant post-processing and manual examination of their output is often required to rule out false-positive predictions and precisely describe mutational events. Results: We have implemented an algorithm for identifying structural variation from DNA resequencing data as part of the breseq computational pipeline for predicting mutations in haploid microbial genomes. Our method evaluates the support for new sequence junctions present in a clonal sample from split-read alignments to a reference genome, including matches to repeat sequences. Then, it uses a statistical model of read coverage evenness to accept or reject these predictions. Finally, breseq combines predictions of new junctions and deleted chromosomal regions to output biologically relevant descriptions of mutations and their effects on genes. We demonstrate the performance of breseq on simulated Escherichia coli genomes with deletions generating unique breakpoint sequences, new insertions of mobile genetic elements, and deletions mediated by mobile elements. Then, we reanalyze data from an E. coli K-12 mutation accumulation evolution experiment in which structural variation was not previously identified. Transposon insertions and large-scale chromosomal changes detected by breseq account for ~25% of spontaneous mutations in this strain. In all cases, we find that breseq is able to reliably predict structural variation with modest read-depth coverage of the reference genome (>40-fold). Conclusions: Using breseq to predict structural variation should be useful for studies of microbial epidemiology, experimental evolution, synthetic biology, and genetics when a reference genome for a closely related strain is available. In these cases, breseq can discover mutations that may be responsible for important or unintended changes in genomes that might otherwise go undetected.", "date": "2014-11-29T00:00:00Z", "citationCount": 90, "authors": [ { "name": "Barrick J.E." }, { "name": "Colburn G." }, { "name": "Deatherage D.E." }, { "name": "Traverse C.C." }, { "name": "Strand M.D." }, { "name": "Borges J.J." }, { "name": "Knoester D.B." }, { "name": "Reba A." }, { "name": "Meyer A.G." } ], "journal": "BMC Genomics" } }, { "doi": "10.1093/nar/gkw343", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.High-throughput data production technologies, particularly 'next-generation' DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1025, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Von Kuster G." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic acids research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, 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Published by Oxford University Press on behalf of Nucleic Acids Research.High-throughput data production technologies, particularly 'next-generation' DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. 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Published by Oxford University Press on behalf of Nucleic Acids Research.High-throughput data production technologies, particularly 'next-generation' DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1025, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Von Kuster G." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic acids research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:24:34Z", "lastUpdate": "2020-06-16T10:55:20Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "extract_archive_merge", "description": "A tool for decompressing an archive file (zip, gz, tar.gz, fastq.gz, fastq.bz2 or tar.bz2) and merging all files into only one.", "homepage": "https://galaxy.pasteur.fr/tool_runner?tool_id=extract_archive_merge", "biotoolsID": "extract_archive_merge", "biotoolsCURIE": "biotools:extract_archive_merge-ip", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" }, { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" }, { "uri": "http://edamontology.org/topic_0607", "term": "Laboratory information management" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "galaxyPasteur" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=extract_archive_merge", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [ { "url": "https://galaxy.pasteur.fr/root?tool_id=extract_archive_merge", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkw343", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.High-throughput data production technologies, particularly 'next-generation' DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. 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Published by Oxford University Press on behalf of Nucleic Acids Research.High-throughput data production technologies, particularly 'next-generation' DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1025, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Von Kuster G." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic acids research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:24:48Z", "lastUpdate": "2020-06-16T10:55:20Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "gdtools_gd2gvf", "description": "Creates a Genome Variation Format (GVF) file of mutations present in an input Genome Diff file.", "homepage": "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html", "biotoolsID": "gdtools_gd2gvf", "biotoolsCURIE": "biotools:gdtools_gd2gvf-ip", "version": [ "0.26" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1975", "term": "GFF3" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_2533", "term": "DNA mutation" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "galaxyPasteur", "gdtools" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/mvalade/gdtools/gdtools_GD2GVF/0.26", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [ { "url": "https://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr%2Frepos%2Fmvalade%2Fgdtools%2Fgdtools_GD2GVF%2F0.26", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/1471-2164-15-1039", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq", "abstract": "© 2014 Barrick et al.Background: Mutations that alter chromosomal structure play critical roles in evolution and disease, including in the origin of new lifestyles and pathogenic traits in microbes. Large-scale rearrangements in genomes are often mediated by recombination events involving new or existing copies of mobile genetic elements, recently duplicated genes, or other repetitive sequences. Most current software programs for predicting structural variation from short-read DNA resequencing data are intended primarily for use on human genomes. They typically disregard information in reads mapping to repeat sequences, and significant post-processing and manual examination of their output is often required to rule out false-positive predictions and precisely describe mutational events. Results: We have implemented an algorithm for identifying structural variation from DNA resequencing data as part of the breseq computational pipeline for predicting mutations in haploid microbial genomes. Our method evaluates the support for new sequence junctions present in a clonal sample from split-read alignments to a reference genome, including matches to repeat sequences. Then, it uses a statistical model of read coverage evenness to accept or reject these predictions. Finally, breseq combines predictions of new junctions and deleted chromosomal regions to output biologically relevant descriptions of mutations and their effects on genes. We demonstrate the performance of breseq on simulated Escherichia coli genomes with deletions generating unique breakpoint sequences, new insertions of mobile genetic elements, and deletions mediated by mobile elements. Then, we reanalyze data from an E. coli K-12 mutation accumulation evolution experiment in which structural variation was not previously identified. Transposon insertions and large-scale chromosomal changes detected by breseq account for ~25% of spontaneous mutations in this strain. In all cases, we find that breseq is able to reliably predict structural variation with modest read-depth coverage of the reference genome (>40-fold). Conclusions: Using breseq to predict structural variation should be useful for studies of microbial epidemiology, experimental evolution, synthetic biology, and genetics when a reference genome for a closely related strain is available. In these cases, breseq can discover mutations that may be responsible for important or unintended changes in genomes that might otherwise go undetected.", "date": "2014-11-29T00:00:00Z", "citationCount": 90, "authors": [ { "name": "Barrick J.E." }, { "name": "Colburn G." }, { "name": "Deatherage D.E." }, { "name": "Traverse C.C." }, { "name": "Strand M.D." }, { "name": "Borges J.J." }, { "name": "Knoester D.B." }, { "name": "Reba A." }, { "name": "Meyer A.G." } ], "journal": "BMC Genomics" } }, { "doi": "10.1093/nar/gkw343", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.High-throughput data production technologies, particularly 'next-generation' DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. 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