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In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1348, "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": "Kuster G.V." }, { "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 } ], "community": null, "owner": "hmenager", "additionDate": "2016-12-19T14:26:26Z", "lastUpdate": "2024-03-08T15:26:38.619142Z", "editPermission": { "type": "public", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SPAdes", "description": "St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.", "homepage": "http://cab.spbu.ru/software/spades/", "biotoolsID": "spades", "biotoolsCURIE": "biotools:spades", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0525", "term": "Genome assembly" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "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_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python" ], "license": "GPL-2.0", "collectionID": [ "SPAdes", "galaxyPasteur", "Animal and Crop Genomics" ], "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/spades/spades/3.9.0", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [ { "url": "http://cab.spbu.ru/files/release3.10.1/manual.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1089/cmb.2012.0021", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing", "abstract": "The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software. © Copyright 2012, Mary Ann Liebert, Inc.", "date": "2012-05-01T00:00:00Z", "citationCount": 15962, "authors": [ { "name": "Bankevich A." }, { "name": "Nurk S." }, { "name": "Antipov D." }, { "name": "Gurevich A.A." }, { "name": "Dvorkin M." }, { "name": "Kulikov A.S." }, { "name": "Lesin V.M." }, { "name": "Nikolenko S.I." }, { "name": "Pham S." }, { "name": "Prjibelski A.D." }, { "name": "Pyshkin A.V." }, { "name": "Sirotkin A.V." }, { "name": "Vyahhi N." }, { "name": "Tesler G." }, { "name": "Alekseyev M.A." }, { "name": "Pevzner P.A." } ], "journal": "Journal of Computational Biology" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": null, "email": "spades.support@cab.spbu.ru", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "matus.kalas@uib.no", "additionDate": "2017-08-20T17:30:35Z", "lastUpdate": "2024-03-08T15:11:04.466129Z", "editPermission": { "type": "public", "authors": [ "animalandcropgenomics", "alexcorm" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "cd-hit", "description": "Cluster a nucleotide dataset into representative sequences.", "homepage": "https://github.com/weizhongli/cdhit", "biotoolsID": "cd-hit", "biotoolsCURIE": "biotools:cd-hit", "version": [ "4.6.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0291", "term": "Sequence clustering" } ], "input": [ { "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_0850", "term": "Sequence set" }, "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" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "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" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/afelten/microbiome_analyses/CD-HIT/4.6.1", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/weizhongli/cdhit/wiki", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bts565", "pmid": "23060610", "pmcid": "PMC3516142", "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/bioinformatics/btl158", "pmid": "16731699", "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/bioinformatics/17.3.282", "pmid": "11294794", "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/bioinformatics/18.1.77", "pmid": "11836214", "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/bioinformatics/btq003", "pmid": "20053844", "pmcid": "PMC2828112", "type": [], "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 } ], "community": null, "owner": "hmenager", "additionDate": "2016-12-19T14:28:27Z", "lastUpdate": "2024-03-06T13:01:07.766440Z", "editPermission": { "type": "group", "authors": [ "sergitobara", "ELIXIR-CZ", "yaominmin" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "RiboGalaxy", "description": "Galaxy-based web server where researchers can pre-process, align, analyze and visualize their own ribosome profiling (ribo-seq) data. GUI-based tools are provided to determine the strength of the triplet periodicity signal in ribo-seq data, generate metagene and ribosome profiles and carry out differential translation expression analysis using the riboSeqR suite. The RUST suite of tools can be used to quickly characterize ribosome profiling datasets to assess their quality and more.", "homepage": "http://ribogalaxy.ucc.ie", "biotoolsID": "ribogalaxy", "biotoolsCURIE": "biotools:ribogalaxy", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_2928", "term": "Alignment" }, { "uri": "http://edamontology.org/operation_0314", "term": "Gene expression profiling" }, { "uri": "http://edamontology.org/operation_2495", "term": "Gene expression analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0848", "term": "Raw sequence" }, "format": [ { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_3006", "term": "bigWig" } ] }, { "data": { "uri": "http://edamontology.org/data_2969", "term": "Sequence image" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" } ] } ], "note": "Raw ribo-seq and mRNA-seq FASTQ files There are multiple outputs depending on the tool/jobs that are run. Most of the ribo-seq analysis tools provide the output in both spreadsheet and/or visual format.", "cmd": null } ], "toolType": [ "Workbench" ], "topic": [ { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" } ], "operatingSystem": [ "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [ "Galaxy" ], "link": [ { "url": "https://github.com/riboseqorg/RiboGalaxy", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "http://ribogalaxy.ucc.ie/static/conditions_of_use.html", "type": [ "Terms of use" ], "note": null }, { "url": "http://ribogalaxy.ucc.ie/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1080/15476286.2016.1141862", "pmid": "26821742", "pmcid": "PMC4829337", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data", "abstract": "Ribosome profiling (ribo-seq) is a technique that uses high-throughput sequencing to reveal the exact locations and densities of translating ribosomes at the entire transcriptome level. The technique has become very popular since its inception in 2009. Yet experimentalists who generate ribo-seq data often have to rely on bioinformaticians to process and analyze their data. We present RiboGalaxy (http://ribogalaxy.ucc.ie), a freely available Galaxy-based web server for processing and analyzing ribosome profiling data with the visualization functionality provided by GWIPS-viz (http://gwips.ucc.ie). RiboGalaxy offers researchers a suite of tools specifically tailored for processing ribo-seq and corresponding mRNA-seq data. Researchers can take advantage of the published workflows which reduce the multi-step alignment process to a minimum of inputs from the user. Users can then explore their own aligned data as custom tracks in GWIPS-viz and compare their ribosome profiles to existing ribo-seq tracks from published studies. In addition, users can assess the quality of their ribo-seq data, determine the strength of the triplet periodicity signal, generate meta-gene ribosome profiles as well as analyze the relative impact of mRNA sequence features on local read density. RiboGalaxy is accompanied by extensive documentation and tips for helping users. In addition we provide a forum (http://gwips.ucc.ie/Forum) where we encourage users to post their questions and feedback to improve the overall RiboGalaxy service.", "date": "2016-03-03T00:00:00Z", "citationCount": 67, "authors": [ { "name": "Michel A.M." }, { "name": "Mullan J.P.A." }, { "name": "Velayudhan V." }, { "name": "O'Connor P.B.F." }, { "name": "Donohue C.A." }, { "name": "Baranov P.V." } ], "journal": "RNA Biology" } }, { "doi": "10.1016/J.JMB.2023.168043", "pmid": "37356899", "pmcid": null, "type": [ "Review" ], "version": null, "note": null, "metadata": { "title": "RiboGalaxy: A Galaxy-based Web Platform for Ribosome Profiling Data Processing – 2023 Update", "abstract": "Ribosome profiling (Ribo-Seq) captures a “snapshot” of ribosomes’ locations at the entire transcriptome of a cell at sub-codon resolution providing insights into gene expression and enabling the discovery of novel translated regions. RiboGalaxy (https://ribogalaxy.genomicsdatascience.ie/), a Galaxy-based platform for processing Ribo-Seq data is a RiboSeq.Org (https://riboseq.org/) resource. RiboSeq.Org is an online gateway to a set of integrated tools for the processing and analysis of Ribo-Seq data. In this RiboGalaxy update we introduce changes to both the tools available on RiboGalaxy and to how the resource is managed on the backend. For example, in order to improve interoperability between Riboseq.Org resources, we added tools that link RiboGalaxy outputs with Trips-Viz and GWIPS-viz browsers for downstream analysis and visualisation. RiboGalaxy's backend now utilises Ansible configuration management which enhances its stability and jobs are executed within Singularity containers and are managed by Slurm, strengthening reproducibility and performance respectively.", "date": "2023-07-15T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Fedorova A.D." }, { "name": "Tierney J.A.S." }, { "name": "Michel A.M." }, { "name": "Baranov P.V." } ], "journal": "Journal of Molecular Biology" } } ], "credit": [ { "name": "Science Foundation Ireland", "email": "info@sfi.ie", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "ucc.ie", "email": null, "url": "http://www.ucc.ie", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "ribogalaxy@gmail.com", "url": "http://ribogalaxy.ucc.ie/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Pavel V. Baranov", "email": "p.baranov@ucc.ie", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "A.Michel@ucc.ie", "additionDate": "2016-05-24T10:51:12Z", "lastUpdate": "2024-02-23T09:02:01.891026Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HMMER hmmscan (EBI)", "description": "HMMER3 hmmscan is used to search sequences against collections of profiles.", "homepage": "https://www.ebi.ac.uk/jdispatcher/pfa/hmmer3_hmmscan", "biotoolsID": "hmmer_hmmscan_ebi", "biotoolsCURIE": "biotools:hmmer_hmmscan_ebi", "version": [ "1" ], "otherID": [], "relation": [ { "biotoolsID": "hmmer3", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0338", "term": "Sequence database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0849", "term": "Sequence record" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1364", "term": "Hidden Markov model" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2066", "term": "Database hits (sequence) format" } ] }, { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0623", "term": "Gene and protein families" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [ "EBI Tools", "Job Dispatcher Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.ebi.ac.uk/about/contact/support/job-dispatcher-services", "type": [ "Helpdesk" ], "note": null } ], "download": [ { "url": "http://hmmer.org/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.ebi.ac.uk/jdispatcher/help", "type": [ "General" ], "note": null }, { "url": "http://hmmer.org/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkr367", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "HMMER web server: Interactive sequence similarity searching", "abstract": "HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. It is now feasible to make efficient profile hidden Markov model (profile HMM) searches via the web. A HMMER web server (http://hmmer.janelia.org) has been designed and implemented such that most protein database searches return within a few seconds. Methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database, and for searching a protein sequence against Pfam. The web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once. All search methods are also available as RESTful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows. We have focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them. © 2011 The Author(s).", "date": "2011-07-01T00:00:00Z", "citationCount": 3538, "authors": [ { "name": "Finn R.D." }, { "name": "Clements J." }, { "name": "Eddy S.R." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkac240", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Search and sequence analysis tools services from EMBL-EBI in 2022", "abstract": "The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. 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