Resource List
List all resources, or create a new resource.
GET /api/t?format=api
{ "count": 30539, "next": "?page=2", "previous": null, "list": [ { "name": "CATS-rf", "description": "CATS-rf evaluates transcriptome assemblies using RNA-seq reads without requiring a reference genome", "homepage": "https://github.com/bodulic/CATS-rf", "biotoolsID": "cats-rf", "biotoolsCURIE": "biotools:cats-rf", "version": [ "1.0.3" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3180", "term": "Sequence assembly validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0951", "term": "Statistical estimate score" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_3391", "term": "Omics" }, { "uri": "http://edamontology.org/topic_3070", "term": "Biology" }, { "uri": "http://edamontology.org/topic_4019", "term": "Biosciences" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "R", "Bash" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/bodulic/CATS-rf", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/bodulic/CATS-rf", "type": "Source code", "note": null, "version": "1.0.2" }, { "url": "https://anaconda.org/bioconda/cats-rf", "type": "Software package", "note": null, "version": "1.0.2" }, { "url": "https://hub.docker.com/repository/docker/bodulic/cats-rf", "type": "Container file", "note": null, "version": "1.0.2" } ], "documentation": [ { "url": "https://github.com/bodulic/CATS-rf", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1101/2025.07.22.666112", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Kristian Bodulić", "email": "kristian.bodulic@gmail.com", "url": "https://orcid.org/0000-0002-1212-3302", "orcidid": "https://orcid.org/0000-0002-1212-3302", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer", "Documentor", "Primary contact" ], "note": null } ], "owner": "bodulic", "additionDate": "2025-09-03T07:50:00.879412Z", "lastUpdate": "2025-09-13T17:36:18.188276Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Atomic Charge Calculator II", "description": "Atomic Charge Calculator II (ACC II) is a web application for fast calculation of partial atomic charges.", "homepage": "https://acc2.ncbr.muni.cz", "biotoolsID": "atomic-charge-calculator-ii", "biotoolsCURIE": "biotools:atomic-charge-calculator-ii", "version": [ "2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3438", "term": "Calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" }, { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" } ] }, { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" } ] } ], "output": [], "note": "Calculation of partial atomic charges", "cmd": null } ], "toolType": [ "Web application", "Web API", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3332", "term": "Computational chemistry" } ], "operatingSystem": [], "language": [ "Python", "JavaScript", "C++" ], "license": "MIT", "collectionID": [ "ELIXIR-CZ" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [ { "url": "https://github.com/krab1k/AtomicChargeCalculator2", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/krab1k/ChargeFW2", "type": [ "Repository" ], "note": "Computational core" } ], "download": [], "documentation": [ { "url": "https://acc2.ncbr.muni.cz/static/manual.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkaa367", "pmid": "32402071", "pmcid": "PMC7319571", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Atomic charge calculator II: Web-based tool for the calculation of partial atomic charges", "abstract": "", "date": "2021-01-01T00:00:00Z", "citationCount": 46, "authors": [], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Radka Svobodová", "email": "radka.svobodova@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-3840-8760", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null }, { "name": "Tomáš Raček", "email": "tomas.racek@muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-0296-2452", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null } ], "owner": "ELIXIR-CZ", "additionDate": "2021-01-18T09:10:00Z", "lastUpdate": "2025-09-11T08:26:42.258113Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "fastplong", "description": "Ultrafast preprocessing and quality control for long reads (Nanopore, PacBio, Cyclone, etc.).", "homepage": "https://github.com/OpenGene/fastplong", "biotoolsID": "fastplong", "biotoolsCURIE": "biotools:fastplong", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3218", "term": "Sequencing quality control" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [], "language": [], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/OpenGene/fastplong", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/OpenGene/fastplong/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1002/imt2.107", "pmid": "38868435", "pmcid": "PMC10989850", "type": [ "Method" ], "version": null, "note": "Mentioned as Citation in the git repository. \nPublication describes only the (short read) tool fastp.", "metadata": { "title": "Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp", "abstract": "", "date": "2023-05-01T00:00:00Z", "citationCount": 716, "authors": [], "journal": "iMeta" } } ], "credit": [ { "name": "OpenGene", "email": null, "url": "https://github.com/OpenGene", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": "OpenGene - Open Source Genomics Toolbox\nOpen source tools for NGS data analysis" } ], "owner": "bart", "additionDate": "2025-09-10T13:36:20.945616Z", "lastUpdate": "2025-09-10T14:13:36.859562Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "REPET", "description": "The REPET package integrates bioinformatics pipelines dedicated to detect, annotate and analyze transposable elements (TEs) in genomic sequences. The main pipelines are (i) TEdenovo, which search for interspersed repeats, build consensus sequences and classify them according to TE features, and (ii)\n TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations exported into GFF3 files.", "homepage": "https://urgi.versailles.inrae.fr/Tools/REPET", "biotoolsID": "repet", "biotoolsCURIE": "biotools:repet", "version": [ "v3.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0379", "term": "Repeat sequence detection" }, { "uri": "http://edamontology.org/operation_0237", "term": "Repeat sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_2206", "term": "Sequence feature table format (text)" } ] }, { "data": { "uri": "http://edamontology.org/data_3002", "term": "Annotation track" }, "format": [ { "uri": "http://edamontology.org/format_1939", "term": "GFF3-seq" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0157", "term": "Sequence composition, complexity and repeats" }, { "uri": "http://edamontology.org/topic_0654", "term": "DNA" }, { "uri": "http://edamontology.org/topic_0097", "term": "Nucleic acid structure analysis" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "C++", "Python" ], "license": "CECILL-2.0", "collectionID": [ "REPET", "elixir-fr-sdp-2019", "URGI" ], "maturity": "Legacy", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://urgi.versailles.inrae.fr/download/repet/", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://urgi.versailles.inrae.fr/download/repet/REPET_linux-x64-3.0.tar.gz", "type": "Source code", "note": null, "version": "v3.0" } ], "documentation": [ { "url": "https://urgi.versailles.inrae.fr/Tools/REPET", "type": [ "General" ], "note": "see also https://urgi.versailles.inrae.fr/Tools/REPET/README" }, { "url": "https://urgi.versailles.inrae.fr/Tools/REPET/INSTALL", "type": [ "Installation instructions" ], "note": null }, { "url": "https://urgi.versailles.inrae.fr/Tools/REPET/TEdenovo-tuto", "type": [ "User manual" ], "note": "See also https://urgi.versailles.inra.fr/Tools/REPET/TEannot-tuto" }, { "url": "https://forgemia.inra.fr/urgi-anagen/wiki-repet/-/wikis/REPET-V3.0-tutorial", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pone.0091929", "pmid": "24786468", "pmcid": "PMC4008368", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PASTEC: An automatic transposable element classification tool", "abstract": "", "date": "2014-05-02T00:00:00Z", "citationCount": 226, "authors": [], "journal": "PLoS ONE" } }, { "doi": "10.1371/journal.pone.0016526", "pmid": "21304975", "pmcid": "PMC3031573", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Considering transposable element diversification in de novo annotation approaches", "abstract": "", "date": "2011-02-09T00:00:00Z", "citationCount": 355, "authors": [], "journal": "PLoS ONE" } }, { "doi": "10.1371/journal.pcbi.0010022", "pmid": "16110336", "pmcid": "PMC1185648", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Combined evidence annotation of transposable elements in genome sequences", "abstract": "", "date": "2005-01-01T00:00:00Z", "citationCount": 279, "authors": [], "journal": "PLoS Computational Biology" } }, { "doi": "10.1007/s00239-003-0007-2", "pmid": "15008403", "pmcid": null, "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "Detection of New Transposable Element Families in Drosophila melanogaster and Anopheles gambiae Genomes", "abstract": "", "date": "2003-12-29T00:00:00Z", "citationCount": 65, "authors": [], "journal": "Journal of Molecular Evolution" } }, { "doi": "10.1109/JPROC.2016.2590833", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "De Novo Annotation of Transposable Elements: Tackling the Fat Genome Issue", "abstract": "", "date": "2017-03-01T00:00:00Z", "citationCount": 18, "authors": [], "journal": "Proceedings of the IEEE" } } ], "credit": [ { "name": "URGI", "email": "urgi-repet@versailles.inrae.fr", "url": "http://urgi.versailles.inrae.fr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Developer", "Contributor", "Maintainer", "Provider", "Support", "Documentor" ], "note": "This tool has a \"Numero de depot APP\": FR 001 480007 000 R P 2008 000 31 235" } ], "owner": "Institut Francais de Bioinform", "additionDate": "2016-03-24T16:22:28Z", "lastUpdate": "2025-09-09T08:10:41.737859Z", "editPermission": { "type": "group", "authors": [ "vjamilloux", "johann_confais", "raphael.flores", "cmichotey" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "PASTEClassifier", "description": "The PASTEClassifier (Pseudo Agent System for Transposable Elements Classification) is a transposable element (TE) classifier searching for structural features. It browses the whole spectrum of possible classifications at order level using Wicker hierarchical system. It is also able to automatically classify other repeated elements like SSR (Simple Sequence Repeats), rDNA or potential repeated host genes. The output is designed to facilitate manual curation by providing to the biologist all characteristics that have been found on each TE sequence.", "homepage": "https://urgi.versailles.inra.fr/Tools/PASTEClassifier", "biotoolsID": "PASTEClassifier", "biotoolsCURIE": "biotools:PASTEClassifier", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0157", "term": "Sequence composition, complexity and repeats" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python", "C++" ], "license": "CECILL-2.0", "collectionID": [ "URGI", "REPET" ], "maturity": "Legacy", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://urgi.versailles.inrae.fr/download/repet/", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://urgi.versailles.inrae.fr/download/repet/PASTEC_linux-x64-2.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://urgi.versailles.inra.fr/Tools/PASTEClassifier/PASTEClassifier-tuto", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pone.0091929", "pmid": "24786468", "pmcid": "PMC4008368", "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "PASTEC: An automatic transposable element classification tool", "abstract": "", "date": "2014-05-02T00:00:00Z", "citationCount": 226, "authors": [], "journal": "PLoS ONE" } } ], "credit": [ { "name": "URGI", "email": "urgi-repet@inrae.fr", "url": "https://urgi.versailles.inrae.fr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Developer", "Contributor", "Maintainer", "Provider", "Support", "Documentor" ], "note": null } ], "owner": "fruitshuang", "additionDate": "2019-12-23T00:50:02Z", "lastUpdate": "2025-09-09T08:10:04.310385Z", "editPermission": { "type": "group", "authors": [ "johann_confais", "cmichotey" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SyntenyViewer", "description": "Comparative genomics-driven translational research tool.", "homepage": "https://urgi.versailles.inrae.fr/synteny", "biotoolsID": "urgi", "biotoolsCURIE": "biotools:urgi", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3745", "term": "Ancestral reconstruction" }, { "uri": "http://edamontology.org/operation_2421", "term": "Database search" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" }, { "uri": "http://edamontology.org/topic_3175", "term": "Structural variation" }, { "uri": "http://edamontology.org/topic_3943", "term": "Paleogenomics" }, { "uri": "http://edamontology.org/topic_0108", "term": "Protein expression" }, { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": "Other", "collectionID": [ "URGI" ], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [ "France" ], "elixirCommunity": [ "Plant Sciences" ], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/database/baad027", "pmid": "37159239", "pmcid": "PMC10167986", "type": [], "version": null, "note": null, "metadata": { "title": "SyntenyViewer: a comparative genomics-driven translational research tool", "abstract": "", "date": "2023-01-01T00:00:00Z", "citationCount": 0, "authors": [], "journal": "Database" } } ], "credit": [ { "name": "Jerome Salse", "email": "jerome.salse@inrae.fr", "url": null, "orcidid": "https://orcid.org/0000-0003-2942-1098", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Raphaël Flores", "email": "raphael.flores@inrae.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-0278-5441", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "URGI", "email": "urgi-support@inrae.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Maintainer" ], "note": null } ], "owner": "raphael.flores", "additionDate": "2024-01-10T12:54:25.092426Z", "lastUpdate": "2025-09-09T08:09:00.018602Z", "editPermission": { "type": "group", "authors": [ "cmichotey" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "HVRLocator", "description": "HVRLocator is a workflow to identify spanning hypervariable region(s) from amplicon sequencing variants or SRA public runs (SRR). It aligns query sequences to a reference E. coli full-length 16S rRNA gene and identifies the spanning region through alignment.", "homepage": "https://github.com/fbcorrea/hvrlocator/", "biotoolsID": "hvrlocator", "biotoolsCURIE": "biotools:hvrlocator", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0632", "term": "Probes and primers" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "CC0-1.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://cloud.sylabs.io/library/jsaraiva/repo/hvrlocator", "type": [ "Repository" ], "note": "Singularity container" } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1101/2025.07.24.666487", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "Kasmanas", "additionDate": "2025-09-08T11:36:08.406899Z", "lastUpdate": "2025-09-08T11:37:45.401286Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Benchmarking graph pipelines", "description": "This tool contains scripts used to perform analyses in the paper \"Towards a Standardized Framework for Pangenome Graph Evaluation: Assessing Crop Plant Pangenome Variation Graph Construction from Multiple Assemblies", "homepage": "https://github.com/KopalliV/Benchmarking_graph_pipelines", "biotoolsID": "benchmarking_graph_pipelines", "biotoolsCURIE": "biotools:benchmarking_graph_pipelines", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "vkopalli", "additionDate": "2025-09-06T12:51:16.338121Z", "lastUpdate": "2025-09-06T12:51:16.340443Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Jalview", "description": "Jalview is a free cross-platform program for multiple sequence alignment editing, visualisation and analysis. Use it to align, view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.", "homepage": "https://www.jalview.org/", "biotoolsID": "Jalview", "biotoolsCURIE": "biotools:Jalview", "version": [ "2.11.5.0" ], "otherID": [], "relation": [ { "biotoolsID": "jabaws", "type": "uses" }, { "biotoolsID": "chimera", "type": "uses" }, { "biotoolsID": "chimerax", "type": "uses" }, { "biotoolsID": "pymol", "type": "uses" }, { "biotoolsID": "bioconda", "type": "includedIn" }, { "biotoolsID": "3d-beacons", "type": "uses" }, { "biotoolsID": "uniprot", "type": "uses" }, { "biotoolsID": "pfam", "type": "uses" }, { "biotoolsID": "ensembl", "type": "uses" }, { "biotoolsID": "pdb", "type": "uses" }, { "biotoolsID": "rfam", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" }, { "uri": "http://edamontology.org/operation_0324", "term": "Phylogenetic tree analysis" }, { "uri": "http://edamontology.org/operation_3081", "term": "Sequence alignment editing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1939", "term": "GFF3-seq" }, { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" }, { "uri": "http://edamontology.org/format_1961", "term": "Stockholm format" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" }, { "uri": "http://edamontology.org/format_1938", "term": "GFF2-seq" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1948", "term": "nbrf/pir" }, { "uri": "http://edamontology.org/format_3774", "term": "BioJSON (Jalview)" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_3313", "term": "BLC" }, { "uri": "http://edamontology.org/format_3311", "term": "RNAML" }, { "uri": "http://edamontology.org/format_1947", "term": "GCG MSF" }, { "uri": "http://edamontology.org/format_3015", "term": "Pileup" }, { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" }, { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] }, { "data": { "uri": "http://edamontology.org/data_0886", "term": "Structure alignment" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1948", "term": "nbrf/pir" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_1961", "term": "Stockholm format" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_3313", "term": "BLC" }, { "uri": "http://edamontology.org/format_3774", "term": "BioJSON (Jalview)" }, { "uri": "http://edamontology.org/format_1947", "term": "GCG MSF" }, { "uri": "http://edamontology.org/format_3015", "term": "Pileup" }, { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" } ] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3466", "term": "EPS" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] } ], "note": "Other Input formats:\nAMSA (.amsa);\nJnetFile (.concise, .jnet);\nPFAM (.pfam);\nSubstitution matrix (.matrix);\nJalview Project File (.jvp);\nJalview Feature File (.features, .jvfeatures);\nJalview Annotations File (.annotations, .jvannotations);\nPredicted Aligned Error (PAE) Matrix File (.json)\n...\nOther Output formats:\nPFAM (.pfam);\nBioJS (.biojs) (interactive HTML/Javascript);\nJalview Project File (.jvp);", "cmd": null } ], "toolType": [ "Desktop application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "GPL-3.0", "collectionID": [ "ELIXIR-UK" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools", "Interoperability" ], "elixirNode": [ "UK" ], "elixirCommunity": [], "link": [ { "url": "https://discourse.jalview.org/", "type": [ "Discussion forum" ], "note": null }, { "url": "https://issues.jalview.org/", "type": [ "Issue tracker" ], "note": null }, { "url": "https://www.jalview.org/development/jalview_develop/", "type": [ "Other" ], "note": "Latest development version" }, { "url": "https://source.jalview.org/crucible/browse/jalview", "type": [ "Repository" ], "note": null }, { "url": "https://twitter.com/Jalview", "type": [ "Social media" ], "note": "Twitter feed" }, { "url": "https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw", "type": [ "Social media" ], "note": "YouTube training videos" } ], "download": [ { "url": "https://www.jalview.org/download", "type": "Downloads page", "note": null, "version": null }, { "url": "https://www.jalview.org/download/source/", "type": "Source code", "note": null, "version": null }, { "url": "https://www.jalview.org/download/?os=all", "type": "Binaries", "note": "Binaries for all platforms", "version": null }, { "url": "https://www.jalview.org/favicon.svg", "type": "Icon", "note": null, "version": null }, { "url": "https://www.jalview.org/download/other/jar/", "type": "Binaries", "note": "Executable JAR file", "version": null } ], "documentation": [ { "url": "https://www.jalview.org/about/citation", "type": [ "Citation instructions" ], "note": null }, { "url": "https://www.jalview.org/training/", "type": [ "Training material" ], "note": "Hands-on exercises, Training courses and Training videos" }, { "url": "https://www.jalview.org/help/faq", "type": [ "FAQ" ], "note": null }, { "url": "https://www.jalview.org/help/documentation/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btp033", "pmid": "19151095", "pmcid": "PMC2672624", "type": [], "version": null, "note": null, "metadata": { "title": "Jalview Version 2-A multiple sequence alignment editor and analysis workbench", "abstract": "", "date": "2009-05-07T00:00:00Z", "citationCount": 7499, "authors": [], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Jim Procter", "email": null, "url": "http://www.lifesci.dundee.ac.uk/people/jim-procter", "orcidid": "https://orcid.org/0000-0002-7865-7382", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Geoff Barton", "email": null, "url": "https://www.lifesci.dundee.ac.uk/people/geoff-barton", "orcidid": "https://orcid.org/0000-0002-9014-5355", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "ben_s", "additionDate": "2019-02-13T17:01:40Z", "lastUpdate": "2025-09-04T13:26:28.643607Z", "editPermission": { "type": "group", "authors": [ "ben_s", "jimprocter" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Metabolite_AutoPlotter", "description": "An application to process and visualise metabolite data in the web-browser.", "homepage": "https://mpietzke.shinyapps.io/autoplotter", "biotoolsID": "metabolite_autoplotter", "biotoolsCURIE": "biotools:metabolite_autoplotter", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_3219", "term": "Read pre-processing" }, { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" }, { "uri": "http://edamontology.org/operation_1812", "term": "Data parsing" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [], "language": [ "R", "C" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s40170-020-00220-x", "pmid": "32670572", "pmcid": "PMC7350678", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "Niclaskn", "additionDate": "2021-01-18T09:39:45Z", "lastUpdate": "2025-09-03T15:29:25.361381Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "CATS-rb", "description": "CATS-rb evaluates transcriptome assemblies using the reference genome of the corresponding species", "homepage": "https://github.com/bodulic/CATS-rb", "biotoolsID": "cats-rb", "biotoolsCURIE": "biotools:cats-rb", "version": [ "1.0.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3180", "term": "Sequence assembly validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0951", "term": "Statistical estimate score" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_3391", "term": "Omics" }, { "uri": "http://edamontology.org/topic_3070", "term": "Biology" }, { "uri": "http://edamontology.org/topic_4019", "term": "Biosciences" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "R", "Bash" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/bodulic/CATS-rb", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/bodulic/CATS-rb", "type": "Source code", "note": null, "version": "1.0.2" }, { "url": "https://anaconda.org/bioconda/cats-rb", "type": "Software package", "note": null, "version": "1.0.2" }, { "url": "https://hub.docker.com/repository/docker/bodulic/cats-rb", "type": "Container file", "note": null, "version": "1.0.2" } ], "documentation": [ { "url": "https://github.com/bodulic/CATS-rb", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1101/2025.07.22.666112", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Kristian Bodulić", "email": "kristian.bodulic@gmail.com", "url": "https://orcid.org/0000-0002-1212-3302", "orcidid": "https://orcid.org/0000-0002-1212-3302", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer", "Documentor", "Primary contact" ], "note": null } ], "owner": "bodulic", "additionDate": "2025-09-03T08:01:20.173602Z", "lastUpdate": "2025-09-03T08:01:20.176094Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AARNet FileSender", "description": "FileSender is an open source web application for sending files of any size, quickly and securely. FileSender is available to all institutions affiliated with the Australian Access Federation (AAF). You can use your institution login details to access and use FileSender.", "homepage": "https://filesender.aarnet.edu.au/", "biotoolsID": "aarnet_filesender", "biotoolsCURIE": "biotools:aarnet_filesender", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": "BSD-3-Clause", "collectionID": [], "maturity": null, "cost": null, "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://www.aarnet.edu.au/filesender", "type": [ "General" ], "note": null }, { "url": "https://www.aarnet.edu.au/news-events?productService=90863", "type": [ "Other" ], "note": null } ], "publication": [], "credit": [ { "name": null, "email": null, "url": "https://support.aarnet.edu.au/hc/en-us/categories/6706994638351-FileSender", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "johangustafsson", "additionDate": "2025-09-03T02:19:20.211779Z", "lastUpdate": "2025-09-03T03:12:57.229210Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "El-MAVEN", "description": "Fast, Robust, and User-Friendly Mass Spectrometry Data Processing Engine for Metabolomics.", "homepage": "https://github.com/ElucidataInc/ElMaven", "biotoolsID": "El-MAVEN", "biotoolsCURIE": "biotools:El-MAVEN", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "GPL-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/ElucidataInc/ElMaven", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/ElucidataInc/ElMaven/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://elucidatainc.github.io/ElMaven/Downloads/", "type": "Binaries", "note": null, "version": null }, { "url": "https://github.com/ElucidataInc/ElMaven/releases", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://elucidatainc.github.io/ElMaven/documentation/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1007/978-1-4939-9236-2_19", "pmid": "31119671", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "EL-MAVEN: A fast, robust, and user-friendly mass spectrometry data processing engine for metabolomics", "abstract": "", "date": "2019-01-01T00:00:00Z", "citationCount": 106, "authors": [], "journal": "Methods in Molecular Biology" } } ], "credit": [ { "name": null, "email": "info@elucidata.io", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": null, "email": "elmaven@elucidata.io", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hans", "additionDate": "2019-08-09T13:14:25Z", "lastUpdate": "2025-09-02T12:37:51.759364Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "OmicFlow", "description": "A generalised data structure for fast and efficient loading and data munching of sparse omics data. The 'OmicFlow' requires an up-front validated metadata template from the user, which serves as a guide to connect all the pieces together by aligning them into a single object that is defined as an 'omics' class. Once this unified structure is established, users can perform manual subsetting, visualization, and statistical analysis, or leverage the automated 'autoFlow' method to generate a comprehensive report.", "homepage": "https://github.com/agusinac/OmicFlow", "biotoolsID": "omicflow", "biotoolsCURIE": "biotools:omicflow", "version": [ "1.3.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/agusinac/OmicFlow/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://github.com/agusinac/OmicFlow", "type": [ "Repository" ], "note": null }, { "url": "https://cran.r-project.org/package=OmicFlow", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://cran.r-project.org/web/packages/OmicFlow/OmicFlow.pdf", "type": [ "User manual" ], "note": null }, { "url": "https://github.com/agusinac/OmicFlow/blob/main/README.md", "type": [ "General" ], "note": "Metadata File Instructions" } ], "publication": [], "credit": [], "owner": "agusinac", "additionDate": "2025-08-20T09:24:38.732312Z", "lastUpdate": "2025-09-02T06:28:57.092837Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "European Health Research Data and Sample Catalogue", "description": "A collaborative effort to integrate the catalogues of diverse EU research projects and networks to accelerate reuse and improve citizens health.", "homepage": "https://molgeniscatalogue.org/", "biotoolsID": "molgenis_european_health_research_data_and_sample_catalogue", "biotoolsCURIE": "biotools:molgenis_european_health_research_data_and_sample_catalogue", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Database portal" ], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1055/s-0042-1742522", "pmid": "36463884", "pmcid": "PMC9719789", "type": [], "version": null, "note": null, "metadata": { "title": "Towards an Interoperable Ecosystem of Research Cohort and Real-world Data Catalogues Enabling Multi-center Studies", "abstract": "", "date": "2022-12-04T00:00:00Z", "citationCount": 10, "authors": [], "journal": "Yearbook of Medical Informatics" } } ], "credit": [], "owner": "EleanorHyde", "additionDate": "2025-03-11T14:55:53.492167Z", "lastUpdate": "2025-09-01T08:50:33.437783Z", "editPermission": { "type": "group", "authors": [ "mswertz", "EleanorHyde" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Bakta", "description": "Rapid & standardized annotation of bacterial genomes, MAGs & plasmids", "homepage": "https://github.com/oschwengers/bakta", "biotoolsID": "bakta", "biotoolsCURIE": "biotools:bakta", "version": [ "v1.11.4" ], "otherID": [], "relation": [ { "biotoolsID": "diamond", "type": "uses" }, { "biotoolsID": "hmmer3", "type": "uses" }, { "biotoolsID": "infernal", "type": "uses" }, { "biotoolsID": "trnascan-se", "type": "uses" }, { "biotoolsID": "blast", "type": "uses" }, { "biotoolsID": "aragorn", "type": "uses" }, { "biotoolsID": "pilercr", "type": "uses" }, { "biotoolsID": "deepsig", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0925", "term": "Sequence assembly" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2914", "term": "Sequence features metadata" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2012", "term": "Sequence coordinates" }, "format": [ { "uri": "http://edamontology.org/format_1975", "term": "GFF3" } ] }, { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1364", "term": "Hidden Markov model" }, "format": [ { "uri": "http://edamontology.org/format_3329", "term": "HMMER3" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_1936", "term": "GenBank format" }, { "uri": "http://edamontology.org/format_1927", "term": "EMBL format" }, { "uri": "http://edamontology.org/format_1975", "term": "GFF3" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2887", "term": "Nucleic acid sequence record" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] }, { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": "bakta --db <db-path> --prefix <prefix> --output <output-path> genome.fasta" } ], "toolType": [ "Command-line tool", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/oschwengers/bakta", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/oschwengers/bakta/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://bioconda.github.io/recipes/bakta/README.html", "type": [ "Other" ], "note": null }, { "url": "https://bakta.computational.bio", "type": [ "Service" ], "note": null } ], "download": [ { "url": "https://zenodo.org/records/14916843", "type": "Other", "note": "Mandatory annotation database", "version": "v6.0" } ], "documentation": [ { "url": "https://github.com/oschwengers/bakta/blob/main/README.md", "type": [ "General" ], "note": null }, { "url": "https://github.com/oschwengers/bakta/blob/main/CONTRIBUTION.md", "type": [ "Contributions policy" ], "note": null }, { "url": "https://github.com/oschwengers/bakta/blob/main/CODE_OF_CONDUCT.md", "type": [ "Code of conduct" ], "note": null }, { "url": "https://bakta.readthedocs.io/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1099/mgen.0.000685", "pmid": "34739369", "pmcid": "PMC8743544", "type": [ "Primary" ], "version": "1.1", "note": null, "metadata": { "title": "Bakta: Rapid and standardized annotation of bacterial genomes via alignment-free sequence identification", "abstract": "", "date": "2021-01-01T00:00:00Z", "citationCount": 582, "authors": [], "journal": "Microbial Genomics" } } ], "credit": [ { "name": "Oliver Schwengers", "email": "oliver.schwengers@cb.jlug.de", "url": "https://github.com/oschwengers", "orcidid": "https://orcid.org/0000-0003-4216-2721", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Justus Liebig University Giessen", "email": null, "url": "https://www.uni-giessen.de", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "oschwengers", "additionDate": "2021-05-08T17:25:21Z", "lastUpdate": "2025-09-01T07:59:35.735958Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-CZ", "bebatut" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Metabolic Atlas", "description": "Metabolic Atlas is a web platform integrating open-source genome scale metabolic models (GEMs) for easy browsing and analysis. The goal is to collect curated GEMs, and to bring these models closer to FAIR principles. The website provides visualisations and comparisons of the GEMs, and links to resources, algorithms, other databases, and more general software applications. Metabolic Atlas is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. In short, the vision is to create a one-stop-shop for everything metabolism related.", "homepage": "https://metabolicatlas.org", "biotoolsID": "metabolicatlas", "biotoolsCURIE": "biotools:metabolicatlas", "version": [ "3.0 - 3.5+", "2.0 - 2.6", "1.0 - 1.7" ], "otherID": [ { "value": "DOI:10.1093/nar/gkac831", "type": "doi", "version": "3.3" } ], "relation": [ { "biotoolsID": "proteinatlas", "type": "usedBy" }, { "biotoolsID": "proteinatlas", "type": "uses" }, { "biotoolsID": "metanetx", "type": "uses" }, { "biotoolsID": "identifiers.org", "type": "uses" }, { "biotoolsID": "metanetx", "type": "usedBy" }, { "biotoolsID": "identifiers.org", "type": "usedBy" }, { "biotoolsID": "chebi", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3926", "term": "Pathway visualisation" }, { "uri": "http://edamontology.org/operation_0573", "term": "Map drawing" }, { "uri": "http://edamontology.org/operation_0533", "term": "Expression profile pathway mapping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [ "Sweden" ], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/MetabolicAtlas/MetabolicAtlas", "type": "Source code", "note": null, "version": null }, { "url": "https://github.com/MetabolicAtlas/MetabolicAtlas/blob/main/frontend/public/img/logo.png", "type": "Icon", "note": null, "version": null }, { "url": "https://metabolicatlas.org/api/v2/", "type": "API specification", "note": null, "version": null } ], "documentation": [ { "url": "https://metabolicatlas.org/documentation", "type": [ "User manual" ], "note": null }, { "url": "https://metabolicatlas.org/api", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1126/scisignal.aaz1482", "pmid": "32209698", "pmcid": "PMC7331181", "type": [], "version": "1", "note": null, "metadata": { "title": "An atlas of human metabolism", "abstract": "", "date": "2020-03-24T00:00:00Z", "citationCount": 253, "authors": [], "journal": "Science Signaling" } }, { "doi": "10.1073/pnas.2102344118", "pmid": "34282017", "pmcid": "PMC8325244", "type": [], "version": "2", "note": null, "metadata": { "title": "Genome-scale metabolic network reconstruction of model animals as a platform for translational research", "abstract": "", "date": "2021-07-27T00:00:00Z", "citationCount": 69, "authors": [], "journal": "Proceedings of the National Academy of Sciences of the United States of America" } }, { "doi": "10.1093/nar/gkac831", "pmid": "36169223", "pmcid": "PMC9825421", "type": [], "version": "3", "note": null, "metadata": { "title": "GotEnzymes: an extensive database of enzyme parameter predictions", "abstract": "", "date": "2023-01-06T00:00:00Z", "citationCount": 35, "authors": [], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/database/bav068", "pmid": "26209309", "pmcid": "PMC4513696", "type": [], "version": "0", "note": null, "metadata": { "title": "Human metabolic atlas: An online resource for human metabolism", "abstract": "", "date": "2015-01-01T00:00:00Z", "citationCount": 66, "authors": [], "journal": "Database" } } ], "credit": [ { "name": "Mihail Anton", "email": "contact@metabolicatlas.org", "url": null, "orcidid": "https://orcid.org/0000-0002-7753-9042", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null } ], "owner": "M", "additionDate": "2020-04-23T07:50:13Z", "lastUpdate": "2025-08-31T22:25:13.264963Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MetaSBT", "description": "MetaSBT is a scalable framework designed to automatically index microbial genomes and accurately characterize metagenome-assembled genomes using Sequence Bloom Trees.", "homepage": "https://github.com/cumbof/MetaSBT", "biotoolsID": "metasbt", "biotoolsCURIE": "biotools:metasbt", "version": [ "0.1.4.post1", "0.1.5" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/cumbof/MetaSBT", "type": [ "Repository" ], "note": "Framework Repository" }, { "url": "https://github.com/cumbof/MetaSBT-DBs", "type": [ "Repository" ], "note": "Repository with Public MetaSBT Databases" } ], "download": [ { "url": "https://pypi.io/packages/source/m/metasbt/metasbt-0.1.4.post1.tar.gz", "type": "Software package", "note": null, "version": "0.1.4" } ], "documentation": [ { "url": "https://github.com/cumbof/MetaSBT/wiki", "type": [ "General" ], "note": "Official MetaSBT Wiki" } ], "publication": [], "credit": [ { "name": "Fabio Cumbo", "email": "fabio.cumbo@gmail.com", "url": "https://cumbof.github.io", "orcidid": "https://orcid.org/0000-0003-2920-5838", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Developer", "Maintainer", "Support" ], "note": null } ], "owner": "fabiocumbo", "additionDate": "2025-06-17T20:53:54.551980Z", "lastUpdate": "2025-08-29T00:30:28.809173Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ProteinProspector", "description": "A suite of protein identification tools.", "homepage": "http://prospector.ucsf.edu", "biotoolsID": "proteinprospector", "biotoolsCURIE": "biotools:proteinprospector", "version": [], "otherID": [ { "value": "RRID:SCR_014558", "type": "rrid", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2929", "term": "Protein fragment weight comparison" }, { "uri": "http://edamontology.org/operation_3647", "term": "Blind peptide database search" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3489", "term": "Database management" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "ms-utils", "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://ms-utils.org", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://prospector.ucsf.edu/prospector/html/instruct/allman.htm", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1074/mcp.d500002-mcp200", "pmid": "15937296", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cells, time-of-flight mass spectrometer: II New developments in protein prospector allow for reliable and comprehensive automatic analysis of large datasets", "abstract": "A thorough analysis of the protein interaction partners of the yeast GTPase Gsp1p was carried out by a multidimensional chromatography strategy of strong cation exchange fractionation of peptides followed by reverse phase LC-ESI-MSMS using a QSTAR instrument. This dataset was then analyzed using the latest developmental version of Protein Prospector. The Prospector search results were also compared with results from the search engine \"Mascot\" using a new results comparison program within Prospector named \"SearchCompare.\" The results from this study demonstrate that the high quality data produced on a quadrupole selecting, quadrupole collision cell, time-of-flight (QqTOF) geometry instrument allows for confident assignment of the vast majority of interpretable spectra by current search engines. © 2005 by The American Society for Biochemistry and Molecular Biology, Inc.", "date": "2005-08-01T00:00:00Z", "citationCount": 165, "authors": [ { "name": "Chalkley R.J." }, { "name": "Baker P.R." }, { "name": "Huang L." }, { "name": "Hansen K.C." }, { "name": "Allen N.P." }, { "name": "Rexach M." }, { "name": "Burlingame A.L." } ], "journal": "Molecular and Cellular Proteomics" } } ], "credit": [ { "name": "Admin", "email": "ppadmin@cgl.ucsf.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": null, "email": "webmaster@ms-utils.org", "url": "http://ms-utils.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": null } ], "owner": "msutils_import", "additionDate": "2017-01-17T14:51:18Z", "lastUpdate": "2025-08-28T15:15:11.245617Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools", "n.m.palmblad@lumc.nl" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "VAPOR", "description": "VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.", "homepage": "https://github.com/wm75/vaporup", "biotoolsID": "vapor", "biotoolsCURIE": "biotools:vapor", "version": [ "1.0.3" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_0524", "term": "De-novo assembly" }, { "uri": "http://edamontology.org/operation_3198", "term": "Read mapping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3673", "term": "Whole genome sequencing" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" } ], "operatingSystem": [], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/connor-lab/vapor", "type": [ "Other" ], "note": "Original VAPOR repository from which versions prior to 1.0.3 were released" } ], "download": [ { "url": "https://pypi.org/project/vaporup/#files", "type": "Software package", "note": null, "version": null }, { "url": "https://doi.org/10.5281/zenodo.15364147", "type": "Biological data", "note": "A curated collection of reference sequences for each influenza A genome segment that can be used with the tool for classification of sequences from this virus", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1093/bioinformatics/btz814", "pmid": "31693070", "pmcid": "PMC7703727", "type": [], "version": null, "note": null, "metadata": { "title": "Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications", "abstract": "Motivation: Influenza viruses represent a global public health burden due to annual epidemics and pandemic potential. Due to a rapidly evolving RNA genome, inter-species transmission, intra-host variation, and noise in short-read data, reads can be lost during mapping, and de novo assembly can be time consuming and result in misassembly. We assessed read loss during mapping and designed a graph-based classifier, VAPOR, for selecting mapping references, assembly validation and detection of strains of non-human origin. Results: Standard human reference viruses were insufficient for mapping diverse influenza samples in simulation. VAPOR retrieved references for 257 real whole-genome sequencing samples with a mean of > 99:8% identity to assemblies, and increased the proportion of mapped reads by up to 13.3% compared to standard references. VAPOR has the potential to improve the robustness of bioinformatics pipelines for surveillance and could be adapted to other RNA viruses.", "date": "2020-01-01T00:00:00Z", "citationCount": 7, "authors": [ { "name": "Southgate J.A." }, { "name": "Bull M.J." }, { "name": "Brown C.M." }, { "name": "Watkins J." }, { "name": "Corden S." }, { "name": "Southgate B." }, { "name": "Moore C." }, { "name": "Connor T.R." } ], "journal": "Bioinformatics" } } ], "credit": [], "owner": "Kigaard", "additionDate": "2020-01-14T09:34:01Z", "lastUpdate": "2025-08-28T14:32:58.093703Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-CZ", "wm75" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Make2D-DB II", "description": "Make2D-DB II is an environment to create, convert, publish, interconnect and keep up-to-date 2D-PAGE databases. The tool offers the possibility to automatically update data related to numerous external data resources. It is also possible to dynamically interconnect several remote databases or projects to form a virtual global database accessible from one single entry point. This tool can also be used to build up 2D-PAGE repositories, accessible by any one from the Web.", "homepage": "https://world-2dpage.expasy.org/make2ddb/", "biotoolsID": "make2d-db_ii", "biotoolsCURIE": "biotools:make2d-db_ii", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" }, { "uri": "http://edamontology.org/operation_3630", "term": "Protein quantification" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Perl" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://world-2dpage.expasy.org/make2ddb/1.Readme_main.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/pmic.200300483", "pmid": "12923769", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The Make 2D-DB II package: Conversion of federated two-dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases", "abstract": "The Make 2D-DB tool has been previously developed to help build federated two-dimensional gel electrophoresis (2-DE) databases on one's own web site. The purpose of our work is to extend the strength of the first package and to build a more efficient environment. Such an environment should be able to fulfill the different needs and requirements arising from both the growing use of 2-DE techniques and the increasing amount of distributed experimental data.", "date": "2003-08-01T00:00:00Z", "citationCount": 27, "authors": [ { "name": "Mostaguir K." }, { "name": "Hoogland C." }, { "name": "Binz P.-A." }, { "name": "Appel R.D." } ], "journal": "Proteomics" } } ], "credit": [ { "name": "ExPASy helpdesk", "email": null, "url": "https://www.expasy.org/support", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2017-12-06T18:14:40Z", "lastUpdate": "2025-08-28T13:43:51.088758Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Swiss Mass Abacus", "description": "Calculator of peptide and glycopeptide masses. It is purposefully kept as simple as a basic calculator executing arithmetic operations.", "homepage": "https://glycoproteome.expasy.org/swiss-mass-abacus/", "biotoolsID": "swiss_mass_abacus", "biotoolsCURIE": "biotools:swiss_mass_abacus", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0417", "term": "Protein post-translation modification site prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0122", "term": "Structural genomics" }, { "uri": "http://edamontology.org/topic_0601", "term": "Protein modifications" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://glycoproteome.expasy.org/swiss-mass-abacus/", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "ExPASy helpdesk", "email": null, "url": "https://www.expasy.org/support", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2017-12-06T18:14:54Z", "lastUpdate": "2025-08-28T13:43:28.119620Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Glydin", "description": "Glydin' compiles and maps information relative to glycoepitopes (glycan determinants) as published in the literature or reported in databases. The output is an interactive network of strucutrally related glycan sub-structures.", "homepage": "https://glycoproteome.expasy.org/epitopes/", "biotoolsID": "glydin", "biotoolsCURIE": "biotools:glydin", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0417", "term": "Protein post-translation modification site prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://glycoproteome.expasy.org/epitopes/", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "ExPASy helpdesk", "email": null, "url": "https://www.expasy.org/support", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2017-12-06T18:14:30Z", "lastUpdate": "2025-08-28T13:41:40.603256Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "IScan", "description": "A package to identify insertion sequences and similar transposable elements, their inverted repeats, and the direct target repeats they generate in entire genomes.", "homepage": "https://www.expasy.org/resources/iscan", "biotoolsID": "iscan", "biotoolsCURIE": "biotools:iscan", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0226", "term": "Annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Linux" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.ieu.uzh.ch/wagner/software/IScan/index.html", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "ExPASy helpdesk", "email": null, "url": "https://www.expasy.org/support", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2017-12-06T18:14:10Z", "lastUpdate": "2025-08-28T13:33:36.585259Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MetaboLink", "description": "A web application for Streamlined Processing and Analysis of Large-Scale Untargeted Metabolomics Data.", "homepage": "https://computproteomics.bmb.sdu.dk/app_direct/MetaboLink/", "biotoolsID": "metabolink", "biotoolsCURIE": "biotools:metabolink", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3557", "term": "Imputation" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0153", "term": "Lipidomics" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/M3Metabolomics/MetaboLink/", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/M3Metabolomics/MetaboLink/wiki", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/BIOINFORMATICS/BTAE459", "pmid": "39018180", "pmcid": "PMC11269424", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "MetaboLink: a web application for streamlined processing and analysis of large-scale untargeted metabolomics data", "abstract": "Motivation: The post-processing and analysis of large-scale untargeted metabolomics data face significant challenges due to the intricate nature of correction, filtration, imputation, and normalization steps. Manual execution across various applications often leads to inefficiencies, human-induced errors, and inconsistencies within the workflow. Results: Addressing these issues, we introduce MetaboLink, a novel web application designed to process LC-MS metabolomics datasets combining established methodologies and offering flexibility and ease of implementation. It offers visualization options for data interpretation, an interface for statistical testing, and integration with PolySTest for further tests and with VSClust for clustering analysis. Availability and implementation: Fully functional tool is publicly available at https://computproteomics.bmb.sdu.dk/Metabolomics/. The source code is available at https://github.com/anitamnd/MetaboLink and a detailed description of the app can be found at https://github.com/anitamnd/MetaboLink/wiki. A tutorial video can be found at https://youtu.be/ZM6j10S6Z8Q.", "date": "2024-07-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Mendes A." }, { "name": "Havelund J.F." }, { "name": "Lemvig J." }, { "name": "Schwammle V." }, { "name": "Faergeman N.J." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Ana Mendes", "email": "anamendesml@outlook.com", "url": null, "orcidid": "https://orcid.org/0009-0008-5170-0927", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Nils J Færgeman", "email": "nils.f@bmb.sdu.dk", "url": null, "orcidid": "https://orcid.org/0000-0002-9281-5287", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Pub2Tools", "additionDate": "2025-07-21T09:43:28.406602Z", "lastUpdate": "2025-08-28T13:24:34.167825Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ASAP", "description": "ASAP (Assemble Species by Automatic Partitioning) is a method to build species partitions from single locus sequence alignments.\nASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity.", "homepage": "https://bioinfo.mnhn.fr/abi/public/asap", "biotoolsID": "asap-assemble", "biotoolsCURIE": "biotools:asap-assemble", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3478", "term": "Phylogenetic reconstruction" }, { "uri": "http://edamontology.org/operation_3200", "term": "DNA barcoding" }, { "uri": "http://edamontology.org/operation_0310", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/operation_3359", "term": "Splitting" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_0637", "term": "Taxonomy" }, { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://bioinfo.mnhn.fr/abi/public/asap/help_asap.html", "type": [ "General" ], "note": null }, { "url": "https://bioinfo.mnhn.fr/abi/public/asap/FAQ_asap.html", "type": [ "FAQ" ], "note": null } ], "publication": [ { "doi": "10.1111/1755-0998.13281", "pmid": "33058550", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "ASAP: assemble species by automatic partitioning", "abstract": "© 2020 John Wiley & Sons LtdHere, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough to split data sets as large 104 sequences into putative species in several minutes. Although grounded in evolutionary theory, ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity. ASAP is a stand-alone program that can be used either through a graphical web-interface or that can be downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP and GMYC) on 10 real COI barcode data sets representing various degrees of challenge (from small and easy cases to large and complicated data sets). We also used Monte-Carlo simulations of a multispecies coalescent framework to assess the strengths and weaknesses of ASAP and the other programs. Through these analyses, we demonstrate that ASAP has the potential to become a major tool for taxonomists as it proposes rapidly in a full graphical exploratory interface relevant species hypothesis as a first step of the integrative taxonomy process.", "date": "2021-02-01T00:00:00Z", "citationCount": 15, "authors": [ { "name": "Puillandre N." }, { "name": "Brouillet S." }, { "name": "Achaz G." } ], "journal": "Molecular Ecology Resources" } } ], "credit": [ { "name": "Nicolas Puillandre", "email": "puillandre@mnhn.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Kigaard", "additionDate": "2021-01-18T11:19:37Z", "lastUpdate": "2025-08-28T07:33:58.127682Z", "editPermission": { "type": "group", "authors": [ "arkamukherjee" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ArrayAnalysis", "description": "ArrayAnalysis is a web-based application for transcriptomic data analysis. It supports the analysis of both microarray and RNA-seq data. The tool may also be installed locally as a desktop app, Docker image, or R package.", "homepage": "https://www.arrayanalysis.org", "biotoolsID": "arrayanalysis.org", "biotoolsCURIE": "biotools:arrayanalysis.org", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "CC-BY-4.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://www.arrayanalysis.org", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkt293", "pmid": "23620278", "pmcid": "PMC3692049", "type": [], "version": null, "note": null, "metadata": { "title": "User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org.", "abstract": "Quality control (QC) is crucial for any scientific method producing data. Applying adequate QC introduces new challenges in the genomics field where large amounts of data are produced with complex technologies. For DNA microarrays, specific algorithms for QC and pre-processing including normalization have been developed by the scientific community, especially for expression chips of the Affymetrix platform. Many of these have been implemented in the statistical scripting language R and are available from the Bioconductor repository. However, application is hampered by lack of integrative tools that can be used by users of any experience level. To fill this gap, we developed a freely available tool for QC and pre-processing of Affymetrix gene expression results, extending, integrating and harmonizing functionality of Bioconductor packages. The tool can be easily accessed through a wizard-like web portal at http://www.arrayanalysis.org or downloaded for local use in R. The portal provides extensive documentation, including user guides, interpretation help with real output illustrations and detailed technical documentation. It assists newcomers to the field in performing state-of-the-art QC and pre-processing while offering data analysts an integral open-source package. Providing the scientific community with this easily accessible tool will allow improving data quality and reuse and adoption of standards.", "date": "2013-01-01T00:00:00Z", "citationCount": 107, "authors": [ { "name": "Eijssen L.M." }, { "name": "Jaillard M." }, { "name": "Adriaens M.E." }, { "name": "Gaj S." }, { "name": "de Groot P.J." }, { "name": "Muller M." }, { "name": "Evelo C.T." } ], "journal": "Nucleic acids research" } }, { "doi": "10.1186/s12864-015-1689-8", "pmid": "26122086", "pmcid": "PMC4486126", "type": [], "version": null, "note": null, "metadata": { "title": "A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal", "abstract": "Background: Illumina whole-genome expression bead arrays are a widely used platform for transcriptomics. Most of the tools available for the analysis of the resulting data are not easily applicable by less experienced users. ArrayAnalysis.org provides researchers with an easy-to-use and comprehensive interface to the functionality of R and Bioconductor packages for microarray data analysis. As a modular open source project, it allows developers to contribute modules that provide support for additional types of data or extend workflows. Results: To enable data analysis of Illumina bead arrays for a broad user community, we have developed a module for ArrayAnalysis.org that provides a free and user-friendly web interface for quality control and pre-processing for these arrays. This module can be used together with existing modules for statistical and pathway analysis to provide a full workflow for Illumina gene expression data analysis. Conclusions: The Illumina bead arrays analysis module is available at http://www.arrayanalysis.org. A user guide, a tutorial demonstrating the analysis of an example dataset, and R scripts are available. The module can be used as a starting point for statistical evaluation and pathway analysis provided on the website or to generate processed input data for a broad range of applications in life sciences research.", "date": "2015-06-30T00:00:00Z", "citationCount": 12, "authors": [ { "name": "Eijssen L.M.T." }, { "name": "Goelela V.S." }, { "name": "Kelder T." }, { "name": "Adriaens M.E." }, { "name": "Evelo C.T." }, { "name": "Radonjic M." } ], "journal": "BMC Genomics" } } ], "credit": [ { "name": "Support Forum", "email": null, "url": "https://www.arrayanalysis.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "jarnokoetsier", "additionDate": "2017-05-16T12:28:07Z", "lastUpdate": "2025-08-28T07:09:05.106319Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "UCPH COVID19 DASHBOARD", "description": "The dashboard provides tools for visualizing the COVID-19 spread in individual countries over time, as well as comparing different countries on a similar time scale. We provide time series of Danish test data. Furthermore, we have implemented an estimator for the actual cumulative number of COVID19 cases for every country -- a.k.a. the dark numbers.", "homepage": "https://shiny.science.ku.dk/pbm/COVID19/", "biotoolsID": "ucph_covid19_dashboard", "biotoolsCURIE": "biotools:ucph_covid19_dashboard", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3324", "term": "Infectious disease" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_0781", "term": "Virology" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "COVID-19" ], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/CSSEGISandData/COVID-19", "type": [ "Repository" ], "note": "COVID19 data" }, { "url": "https://www.ssi.dk/aktuelt/sygdomsudbrud/coronavirus/covid-19-i-danmark-epidemiologisk-overvaagningsrapport", "type": [ "Other" ], "note": "SSI data reports" }, { "url": "https://www.worldometers.info/world-population/population-by-country/", "type": [ "Other" ], "note": "Population data" } ], "download": [], "documentation": [ { "url": "https://github.com/CSSEGISandData/COVID-19", "type": [ "Terms of use" ], "note": null }, { "url": "https://github.com/nikolajthams/COVID-19/blob/master/wirvsvirus/draft/concept_online_version.pdf", "type": [ "Other" ], "note": "Analysis white paper" } ], "publication": [], "credit": [ { "name": "Nikolaj Theodor Thams", "email": "thams@math.ku.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Martin Emil Jakobsen", "email": "m.jakobsen@math.ku.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Phillip Bredahl Mogensen", "email": "pbm@math.ku.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Copenhagen Causality Lab (CoCaLa)", "email": null, "url": "https://www.math.ku.dk/english/research/spt/cocala/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "Johns Hopkins University", "email": null, "url": "https://www.jhu.edu/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Danish State Serum Institute (SSI)", "email": null, "url": "https://www.ssi.dk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Pbm", "additionDate": "2020-03-27T14:31:47Z", "lastUpdate": "2025-08-27T10:53:04.522927Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "fqseqpair", "description": "List names of sequence pairs from two FASTQ formatted files.", "homepage": "http://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README", "biotoolsID": "fqseqpair", "biotoolsCURIE": "biotools:fqseqpair", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1933", "term": "FASTQ-solexa" }, { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1933", "term": "FASTQ-solexa" }, { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "galaxyPasteur", "Institut Pasteur", "fqtools" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/fqtools/fqseqpair/1.0", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [], "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": "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": 1477, "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 } ], "owner": "hmenager", "additionDate": "2016-12-19T14:28:48Z", "lastUpdate": "2025-08-27T10:52:16.324100Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "fqseqname", "description": "List names of sequences from FASTQ formatted files.", "homepage": "http://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README", "biotoolsID": "fqseqname", "biotoolsCURIE": "biotools:fqseqname", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Data formatting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1933", "term": "FASTQ-solexa" }, { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" }, { "uri": "http://edamontology.org/topic_0077", "term": "Nucleic acids" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "galaxyPasteur", "Institut Pasteur", "fqtools" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/fqtools/fqseqname/1.0", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [], "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": "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": 1477, "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 } ], "owner": "hmenager", "additionDate": "2016-12-19T14:29:17Z", "lastUpdate": "2025-08-27T10:51:46.964250Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "fqquality", "description": "Output reads with low quality bases trimmed (at the extremities) or masked and/or with quality descreased to the minimum. Output an extra singlet dataset if paired-end data provided.", "homepage": "http://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README", "biotoolsID": "fqquality", "biotoolsCURIE": "biotools:fqquality", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" }, { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" }, { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" }, { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "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" } ] }, { "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_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "galaxyPasteur", "Institut Pasteur", "fqtools" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/fqtools/fqquality/1.0", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [], "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": "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": 1477, "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 } ], "owner": "hmenager", "additionDate": "2016-12-19T14:29:40Z", "lastUpdate": "2025-08-27T10:51:05.950208Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "fqextract", "description": "Extract a subset of fastq reads.", "homepage": "http://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README", "biotoolsID": "fqextract", "biotoolsCURIE": "biotools:fqextract", "version": [ "1.0.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] }, { "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_1931", "term": "FASTQ-illumina" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3077", "term": "Data acquisition" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "galaxyPasteur", "Institut Pasteur", "fqtools" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/fqtools/fqextract/1.0.1", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [], "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": "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": 1477, "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 } ], "owner": "hmenager", "additionDate": "2016-12-19T14:23:06Z", "lastUpdate": "2025-08-27T10:49:53.830123Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "fqduplicate", "description": "Detect duplicate reads. Outputs a list of read names corresponding to reads already seen in the dataset with a better quality sum score (duplicates).", "homepage": "http://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README", "biotoolsID": "fqduplicate", "biotoolsCURIE": "biotools:fqduplicate", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3218", "term": "Sequencing quality control" }, { "uri": "http://edamontology.org/operation_3230", "term": "Read depth analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" }, { "uri": "http://edamontology.org/topic_0077", "term": "Nucleic acids" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "galaxyPasteur", "Institut Pasteur", "fqtools" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/fqtools/fqduplicate/1.0", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [], "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": "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": 1477, "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 } ], "owner": "hmenager", "additionDate": "2016-12-19T14:22:09Z", "lastUpdate": "2025-08-27T10:49:28.510179Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "fqconvert", "description": "Convert quality scoring to Sanger in FASTQ files.", "homepage": "http://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README", "biotoolsID": "fqconvert", "biotoolsCURIE": "biotools:fqconvert", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0233", "term": "Sequence conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1933", "term": "FASTQ-solexa" }, { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] }, { "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_3168", "term": "Sequencing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "galaxyPasteur", "Institut Pasteur", "fqtools" ], "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/fqconvert2/fqconvert/1.0.0", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [], "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": "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": 1477, "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 } ], "owner": "hmenager", "additionDate": "2016-12-19T14:24:18Z", "lastUpdate": "2025-08-27T10:48:08.675794Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "fqcleaner", "description": "Mini workflow for preprocessing fastq files, it includes quality trimming, duplicate and artefacts filters for FASTQ read files.", "homepage": "https://gensoft.pasteur.fr/docs/fqCleanER/21.10/", "biotoolsID": "fqcleaner", "biotoolsCURIE": "biotools:fqcleaner", "version": [ "0.4.1.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" }, { "uri": "http://edamontology.org/operation_3695", "term": "Data filtering" } ], "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_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "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_1932", "term": "FASTQ-sanger" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "galaxyPasteur", "Institut Pasteur", "fqtools" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/fqcleaner/fqCleaner/0.4.1.1", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [], "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": "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": 1477, "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 } ], "owner": "hmenager", "additionDate": "2016-12-19T14:27:26Z", "lastUpdate": "2025-08-27T10:47:14.412802Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CoCoCoNet", "description": "CoCoCoNet iis a tool for identifying conserved gene modules and co mparing co -expression networks. CoCoCoNet is a resource for both data and methods, providing gold-standard networks and sophisticated tools for on-the-fly comparative analyses across 14 species.", "homepage": "https://milton.cshl.edu/CoCoCoNet/", "biotoolsID": "cococonet", "biotoolsCURIE": "biotools:cococonet", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3463", "term": "Expression correlation analysis" }, { "uri": "http://edamontology.org/operation_3927", "term": "Network analysis" }, { "uri": "http://edamontology.org/operation_2436", "term": "Gene-set enrichment analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" }, { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" } ], "operatingSystem": [], "language": [ "R" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/johnlee4/CoCoCoNet", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/johnlee4/CoCoCoNet", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkaa348", "pmid": "32392296", "pmcid": "PMC7319556", "type": [], "version": null, "note": null, "metadata": { "title": "CoCoCoNet: Conserved and comparative co-expression across a diverse set of species", "abstract": "Co-expression analysis has provided insight into gene function in organisms from Arabidopsis to zebrafish. Comparison across species has the potential to enrich these results, for example by prioritizing among candidate human disease genes based on their network properties or by finding alternative model systems where their co-expression is conserved. Here, we present CoCoCoNet as a tool for identifying conserved gene modules and comparing co-expression networks. CoCoCoNet is a resource for both data and methods, providing gold standard networks and sophisticated tools for on-the-fly comparative analyses across 14 species. We show how CoCoCoNet can be used in two use cases. In the first, we demonstrate deep conservation of a nucleolus gene module across very divergent organisms, and in the second, we show how the heterogeneity of autism mechanisms in humans can be broken down by functional groups and translated to model organisms. CoCoCoNet is free to use and available to all at https://milton.cshl.edu/CoCoCoNet, with data and R scripts available at ftp://milton.cshl.edu/data.", "date": "2021-01-01T00:00:00Z", "citationCount": 32, "authors": [ { "name": "Lee J." }, { "name": "Shah M." }, { "name": "Ballouz S." }, { "name": "Crow M." }, { "name": "Gillis J." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Jesse Gillis", "email": "jgillis@cshl.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Kigaard", "additionDate": "2021-01-18T08:31:27Z", "lastUpdate": "2025-08-27T10:44:27.458203Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "datmat", "description": "‘datmat’ is a Python package aimed to easily gather data from a variety of sources and materialize it into a standardized format. It can download projects of imaging data from XNAT into the EUCAIM folder structure, and is designed to be extendible to support other inputs and outputs.", "homepage": "https://gitlab.com/radiology/infrastructure/data-materialisation/", "biotoolsID": "datmat", "biotoolsCURIE": "biotools:datmat", "version": [ "0.2.0" ], "otherID": [], "relation": [ { "biotoolsID": "xnatpy", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3802", "term": "Data sorting" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://pypi.org/project/datmat/", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "https://pypi.org/project/datmat/", "type": "Software package", "note": null, "version": null }, { "url": "https://gitlab.com/radiology/infrastructure/data-materialisation", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://datmat.readthedocs.io/latest/", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "Alexander Harms", "email": "alexander.harms@health-ri.nl", "url": null, "orcidid": "https://orcid.org/0009-0001-5727-6732", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Hakim Achterberg", "email": "h.achterberg@erasmusmc.nl", "url": null, "orcidid": "https://orcid.org/0000-0003-3772-4582", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Erasmus MC", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": "018906e22", "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null } ], "owner": "agjharms", "additionDate": "2025-08-25T14:36:13.568250Z", "lastUpdate": "2025-08-26T09:43:49.092198Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Single-cell multi-scale clustering (MSC)", "description": "Single-cell multi-scale clustering framework published in GigaScience.", "homepage": "https://github.com/songlabcodes/MSC", "biotoolsID": "single-cell_multi-scale_clustering_msc", "biotoolsCURIE": "biotools:single-cell_multi-scale_clustering_msc", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "songw01", "additionDate": "2025-08-25T21:19:45.632393Z", "lastUpdate": "2025-08-25T21:19:45.634805Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "img2catalog", "description": "This tool, 'img2catalog', is built to extract metadata from imaging data repositories, map it to a model class, and export it to a catalog. The tool is set up to be modular, but it currently supports extracting metadata from an XNAT server, converting it to the Health-RI Core v2 metadata model (https://github.com/Health-RI/health-ri-metadata/tree/v2.0.0), based on DCAT-AP v3 and Health-DCAT AP, as defined in Pydantic classes using SeMPyRO (https://github.com/Health-RI/SeMPyRO), and either writing it to an RDF file, or pushing it to a FAIR Data Point (FDP).", "homepage": "https://github.com/Health-RI/img2catalog", "biotoolsID": "img2catalog", "biotoolsCURIE": "biotools:img2catalog", "version": [ "1.0.1" ], "otherID": [], "relation": [ { "biotoolsID": "xnatpy", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_1812", "term": "Data parsing" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_4012", "term": "FAIR data" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/Health-RI/img2catalog", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/Health-RI/img2catalog", "type": "Source code", "note": null, "version": null }, { "url": "https://pypi.org/project/img2catalog/", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/Health-RI/img2catalog/blob/main/README.md", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "Alexander Harms", "email": "alexander.harms@health-ri.nl", "url": null, "orcidid": "https://orcid.org/0009-0001-5727-6732", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Health-RI", "email": null, "url": "https://www.health-ri.nl/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null } ], "owner": "agjharms", "additionDate": "2025-08-25T14:46:01.217831Z", "lastUpdate": "2025-08-25T14:46:01.219964Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ViromeXplore", "description": "ViromeXplore conatains a set of bioinformatic workflows that can be used reproducibly, sequentially and interoperably between them and with other workflows. It allows multiple input types mand starting points that include raw reads, contigs, genomes, abbundance tables, phylogenies and taxonomies. ViromeXplore contains the most varied and comprehensive workflows to explore viral genes and genomes from viromes and metagenomes to date. The future aim for ViromeXplore is to continue expanding the workflows and including the most recent and efficient tools.\n\nThe workflows are implemented in Nextflow, and additionally only Docker or Singularity are needed to run ViromeXplore.", "homepage": "https://viromexplore.readthedocs.io", "biotoolsID": "viromexplore", "biotoolsCURIE": "biotools:viromexplore", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": "BSD-3-Clause", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/rhernandvel/ViromeXplore", "type": [ "Repository" ], "note": "Github repo" } ], "download": [ { "url": "https://github.com/rhernandvel/ViromeXplore", "type": "Other", "note": "Download via github", "version": "1.0.0" } ], "documentation": [ { "url": "https://viromexplore.readthedocs.io", "type": [ "User manual" ], "note": "All the updated documentation can be found in readthedocs." } ], "publication": [], "credit": [ { "name": "Rodrigo Hernández Velázquez", "email": "rhernandvel@gmail.com", "url": null, "orcidid": "https://orcid.org/0009-0009-3048-8573", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "rhernandvel", "additionDate": "2025-08-22T12:42:23.841729Z", "lastUpdate": "2025-08-22T12:53:03.396154Z", "editPermission": { "type": "group", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "EssSubgraph", "description": "EssSubgraph is a model algorithm that integrates omics data and network data to predict essential genes.", "homepage": "https://github.com/wenmm/EssSubgraph/tree/main", "biotoolsID": "esssubgraph", "biotoolsCURIE": "biotools:esssubgraph", "version": [], "otherID": [], "relation": [ { "biotoolsID": "MTGCN", "type": "includes" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0276", "term": "Protein interaction network analysis" } ], "input": [], "output": [], "note": null, "cmd": "python EssSubgraph.py --epochs 200 --device 0 --dataset ./data/esssubgraph_human_pc50_string.pkl" }, { "operation": [ { "uri": "http://edamontology.org/operation_2454", "term": "Gene prediction" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2949", "term": "Protein-protein interaction analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3360", "term": "Biomarkers" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/wenmm/EssSubgraph/tree/main", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/wenmm/EssSubgraph/tree/main", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/wenmm/EssSubgraph/tree/main", "type": [ "Installation instructions" ], "note": null } ], "publication": [ { "doi": "10.1101/2025.07.21.665218", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": null, "note": "https://www.biorxiv.org/content/10.1101/2025.07.21.665218v1.abstract", "metadata": null } ], "credit": [ { "name": "haimei wen", "email": "hudie.luoluo@gmail.com", "url": null, "orcidid": "https://orcid.org/0009-0006-1600-1210", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Susan Carpenter", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-5600-5404", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Karen McGinnis", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-9564-8146", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Andrew Nelson", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-9896-1739", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Keriayn Smith", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-4351-2765", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Tian Hong", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-8212-7050", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null } ], "owner": "haimei", "additionDate": "2025-08-20T17:28:51.309591Z", "lastUpdate": "2025-08-20T18:13:15.065957Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PanGIA", "description": "PanGIA is a deep learning model for predicting ncRNA-disease associations.", "homepage": "https://github.com/qiankunzizairen/PanGIA", "biotoolsID": "rna-disease-predictor", "biotoolsCURIE": "biotools:rna-disease-predictor", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "qiankunzizairen", "additionDate": "2025-08-19T13:03:53.135066Z", "lastUpdate": "2025-08-19T13:04:41.970631Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GenomiX", "description": "VE3's Genomics Accelerator Solution optimizes genomic data processing and storage across AWS, GCP, and Azure, using advanced tools and services.", "homepage": "https://www.ve3.global/", "biotoolsID": "ve3-genomix", "biotoolsCURIE": "biotools:ve3-genomix", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "GenomiX", "additionDate": "2025-08-18T11:50:36.465851Z", "lastUpdate": "2025-08-18T11:50:51.907919Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MRanalysis", "description": "MRanalysis is a comprehensive and user-friendly, web-based platform that provides the first integrated and standardized Mendelian randomization (MR) analysis workflow. This includes GWAS data quality assessment, power/ sample size estimation, MR analysis, SNP-to-gene enrichment analysis, and data visualization. Built using the R shiny framework, MRanalysis enables users to conduct common MR methods, including univariable, multivariable, and mediation MR analyses through an intuitive, no-code interface .", "homepage": "https://mranalysis.cn/", "biotoolsID": "mranalysis", "biotoolsCURIE": "biotools:mranalysis", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "xingabao", "additionDate": "2025-08-17T08:01:46.684554Z", "lastUpdate": "2025-08-17T08:01:56.819327Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MatHeat", "description": "MatHeat transforms your gene expression data into powerful insights, delivering interactive heatmaps, DEG analysis, volcano plots, advanced clustering, UMAP/K-Means, and Reactome pathway exploration.", "homepage": "https://matheat.streamlit.app/", "biotoolsID": "matheat", "biotoolsCURIE": "biotools:matheat", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3574", "term": "Human genetics" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_3372", "term": "Software engineering" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://matheat.streamlit.app/", "type": [ "Service" ], "note": null }, { "url": "https://amin-mat.github.io/matheat-landing/", "type": [ "Other" ], "note": "Landing page of the MatHeat" }, { "url": "https://matheat.org/", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Seyyed Amin Seyyed Rezaei", "email": "seyyedamin1381@gmail.com", "url": "https://matheat.streamlit.app/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact", "Maintainer" ], "note": null } ], "owner": "Aminn", "additionDate": "2025-03-12T22:55:02.224894Z", "lastUpdate": "2025-08-13T11:45:03.617916Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "nf-CBRA-snvs", "description": "Workflow optimized for the analysis of rare diseases, designed to detect SNVs and INDELs in targeted sequencing data (CES/WES) and whole genome sequencing (WGS), built on Nextflow.", "homepage": "https://github.com/CIBERER/nf-CBRA-snvs", "biotoolsID": "nf-cbra-snvs", "biotoolsCURIE": "biotools:nf-cbra-snvs", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux" ], "language": [], "license": "MIT", "collectionID": [ "IMPaCT-Data" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/CIBERER/nf-CBRA-snvs", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/CIBERER/nf-CBRA-snvs", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [], "owner": "pminguez", "additionDate": "2025-08-12T09:03:01.228796Z", "lastUpdate": "2025-08-12T09:05:51.626707Z", "editPermission": { "type": "group", "authors": [ "yolandabq" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "WHALE-FJD", "description": "Pipeline based on Nextflow and nf-core for long-read DNA sequencing analysis.", "homepage": "https://github.com/TBLabFJD/WHALE", "biotoolsID": "whale-fjd", "biotoolsCURIE": "biotools:whale-fjd", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux" ], "language": [], "license": "CC-BY-SA-4.0", "collectionID": [ "IMPaCT-Data" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/TBLabFJD/WHALE", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/TBLabFJD/WHALE", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [], "owner": "pminguez", "additionDate": "2025-08-12T08:52:25.808752Z", "lastUpdate": "2025-08-12T09:05:33.311501Z", "editPermission": { "type": "group", "authors": [ "yolandabq" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PARROT-FJD", "description": "Germline variant calling pipeline implemented in Nextflow which performs mapping, SNV/INDEL calling and annotation, and CNV calling and annotation for targeted sequencing (gene panels and WES) and whole genome sequencing.", "homepage": "https://github.com/TBLabFJD/PARROT-FJD", "biotoolsID": "parrot-fjd", "biotoolsCURIE": "biotools:parrot-fjd", "version": [], "otherID": [], "relation": [ { "biotoolsID": "fjd-pipeline", "type": "isNewVersionOf" }, { "biotoolsID": "priorr", "type": "usedBy" } ], "function": [], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [], "language": [], "license": "CC-BY-NC-4.0", "collectionID": [ "IMPaCT-Data" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [], "elixirCommunity": [ "Rare Diseases" ], "link": [ { "url": "https://github.com/TBLabFJD/PARROT-FJD", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/TBLabFJD/PARROT-FJD", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [], "owner": "pminguez", "additionDate": "2024-06-19T09:33:56.106410Z", "lastUpdate": "2025-08-12T08:35:30.388356Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FJD-pipeline", "description": "Pipeline for Single Nucleotide Variants (SNVs) and Copy Number Variation (CNVs) variant calling. This tool is no longer maintained. See the new version: PARROT-FJD.", "homepage": "https://github.com/TBLabFJD/VariantCallingFJD", "biotoolsID": "fjd-pipeline", "biotoolsCURIE": "biotools:fjd-pipeline", "version": [], "otherID": [], "relation": [ { "biotoolsID": "priorr", "type": "usedBy" }, { "biotoolsID": "parrot-fjd", "type": "hasNewVersion" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3227", "term": "Variant calling" }, { "uri": "http://edamontology.org/operation_3961", "term": "Copy number variation detection" }, { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1193", "term": "Tool name (FASTA)" }, "format": [ { "uri": "http://edamontology.org/format_2545", "term": "FASTQ-like format" } ] } ], "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": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python", "R", "Bash" ], "license": "CC-BY-NC-SA-4.0", "collectionID": [ "IMPaCT-Data" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/TBLabFJD/VariantCallingFJD", "type": [ "Repository" ], "note": "GitHub repository" } ], "download": [], "documentation": [ { "url": "https://github.com/TBLabFJD/VariantCallingFJD", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1038/s41525-021-00278-6", "pmid": "35087072", "pmcid": "PMC8795168", "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "An evaluation of pipelines for DNA variant detection can guide a reanalysis protocol to increase the diagnostic ratio of genetic diseases", "abstract": "Clinical exome (CE) sequencing has become a first-tier diagnostic test for hereditary diseases; however, its diagnostic rate is around 30–50%. In this study, we aimed to increase the diagnostic yield of CE using a custom reanalysis algorithm. Sequencing data were available for three cohorts using two commercial protocols applied as part of the diagnostic process. Using these cohorts, we compared the performance of general and clinically relevant variant calling and the efficacy of an in-house bioinformatic protocol (FJD-pipeline) in detecting causal variants as compared to commercial protocols. On the whole, the FJD-pipeline detected 99.74% of the causal variants identified by the commercial protocol in previously solved cases. In the unsolved cases, FJD-pipeline detects more INDELs and non-exonic variants, and is able to increase the diagnostic yield in 2.5% and 3.2% in the re-analysis of 78 cancer and 62 cardiovascular cases. These results were considered to design a reanalysis, filtering and prioritization algorithm that was tested by reassessing 68 inconclusive cases of monoallelic autosomal recessive retinal dystrophies increasing the diagnosis by 4.4%. In conclusion, a guided NGS reanalysis of unsolved cases increases the diagnostic yield in genetic disorders, making it a useful diagnostic tool in medical genetics.", "date": "2022-12-01T00:00:00Z", "citationCount": 12, "authors": [ { "name": "Romero R." }, { "name": "de la Fuente L." }, { "name": "Del Pozo-Valero M." }, { "name": "Riveiro-Alvarez R." }, { "name": "Trujillo-Tiebas M.J." }, { "name": "Martin-Merida I." }, { "name": "Avila-Fernandez A." }, { "name": "Iancu I.-F." }, { "name": "Perea-Romero I." }, { "name": "Nunez-Moreno G." }, { "name": "Damian A." }, { "name": "Rodilla C." }, { "name": "Almoguera B." }, { "name": "Corton M." }, { "name": "Ayuso C." }, { "name": "Minguez P." } ], "journal": "npj Genomic Medicine" } } ], "credit": [ { "name": "Bioinformatics Unit IIS-FJD", "email": "pablo.minguez@quironsalud.es", "url": "https://www.translationalbioinformaticslab.es/", "orcidid": "https://orcid.org/0000-0003-4099-9421", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "iiancu", "additionDate": "2022-03-21T17:29:40.559556Z", "lastUpdate": "2025-08-12T08:31:29.574795Z", "editPermission": { "type": "group", "authors": [ "gonumo", "pminguez", "yolandabq" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MacSyLib", "description": "a Python package library that allow to model and detect macromolecular systems, genetic pathways… by similarity search in prokaryotes datasets.", "homepage": "https://github.com/gem-pasteur/macsylib", "biotoolsID": "macsylib", "biotoolsCURIE": "biotools:macsylib", "version": [ "1.0.1" ], "otherID": [], "relation": [ { "biotoolsID": "macsyfinder", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3672", "term": "Gene functional annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3949", "term": "Profile HMM" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1245", "term": "Sequence cluster (protein)" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0085", "term": "Functional genomics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [ "GEM Pasteur" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/gem-pasteur/macsylib", "type": [ "Repository" ], "note": null }, { "url": "https://pypi.org/project/MacSyLib/", "type": [ "Other" ], "note": null }, { "url": "https://macsylib.readthedocs.io/en/latest/", "type": [ "Other" ], "note": null } ], "download": [ { "url": "https://github.com/gem-pasteur/macsylib", "type": "Source code", "note": null, "version": "1.0.1" }, { "url": "https://pypi.org/project/MacSyLib/", "type": "Software package", "note": null, "version": "1.0.1" } ], "documentation": [ { "url": "https://macsylib.readthedocs.io/en/latest/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.24072/pcjournal.250", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes", "abstract": "Complex cellular functions are usually encoded by a set of genes in one or a few orga-nized genetic loci in microbial genomes. Macromolecular System Finder (MacSyFinder) is a program that uses these properties to model and then annotate cellular functions in microbial genomes. This is done by integrating the identification of each individual gene at the level of the molecular system. We hereby present a major release of MacSyFinder (version 2) coded in Python 3. The code was improved and rationalized to facilitate future maintainability. Several new features were added to allow more flexible modelling of the systems. We introduce a more intuitive and comprehensive search engine to identify all the best candidate systems and sub-optimal ones that respect the models’ constraints. We also introduce the novel macsydata companion tool that enables the easy installation and broad distribution of the models developed for MacSyFinder (macsy-models) from GitHub repositories. Finally, we have updated and improved MacSyFinder popular mod-els: TXSScan to identify protein secretion systems, TFFscan to identify type IV filaments, CONJscan to identify conjugative systems, and CasFinder to identify CRISPR associated proteins. MacSyFinder and the updated models are available at: https://github.com/gem-pasteur/macsyfinder.", "date": "2023-01-01T00:00:00Z", "citationCount": 43, "authors": [ { "name": "Neron B." }, { "name": "Denise R." }, { "name": "Coluzzi C." }, { "name": "Touchon M." }, { "name": "Rocha E.P.C." }, { "name": "Abby S.S." } ], "journal": "Peer Community Journal" } } ], "credit": [ { "name": "Institut Pasteur", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": "0495fxg12", "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null }, { "name": "Microbial Evolutionary Genomics Unit", "email": null, "url": "https://research.pasteur.fr/en/team/microbial-evolutionary-genomics/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [], "note": null }, { "name": "Bioinformatics and Biostatistics HUB", "email": null, "url": "https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [], "note": null }, { "name": "Eduardo P.C. Rocha", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-7704-822X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Sophie Abby", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-5231-3346", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Bertrand Néron", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-0220-0482", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "bneron", "additionDate": "2025-08-07T10:25:22.118390Z", "lastUpdate": "2025-08-11T12:14:42.322020Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }
