count: 215 list: - accessibility: Open access (with restrictions) additionDate: '2021-03-31T15:26:55Z' biotoolsCURIE: biotools:biomas_bioinformatic_analysis_of_metagenomic_amplicons biotoolsID: biomas_bioinformatic_analysis_of_metagenomic_amplicons collectionID: [] community: null confidence_flag: tool cost: Free of charge (with restrictions) credit: - email: b.fosso@ibiom.cnr.it fundrefid: null gridid: null name: Bruno Fosso note: Researcher at CNR-IBIOM orcidid: https://orcid.org/0000-0003-2324-086X rorid: null typeEntity: Person typeRole: - Developer url: null - email: graziano.pesole@uniba.it fundrefid: null gridid: null name: Graziano Pesole note: Full Professor of Molecular Biology at University of Bari orcidid: https://orcid.org/0000-0003-3663-0859 rorid: null typeEntity: Person typeRole: - Primary contact url: null - email: m.santamaria@ibiom.cnr.it fundrefid: null gridid: null name: Monica Santamaria note: Researcher at CNR-IBIOM orcidid: https://orcid.org/0000-0003-1488-6052 rorid: null typeEntity: Person typeRole: - Contributor url: null description: BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills. documentation: [] download: [] editPermission: authors: [] type: private elixirCommunity: - Marine Metagenomics elixirNode: - Italy elixirPlatform: - Tools elixir_badge: 0 function: - cmd: null input: - data: term: Nucleic acid sequence alignment uri: http://edamontology.org/data_1383 format: - term: SAM uri: http://edamontology.org/format_2573 note: null operation: - term: Taxonomic classification uri: http://edamontology.org/operation_3460 output: - data: term: Taxonomy uri: http://edamontology.org/data_3028 format: - term: newick uri: http://edamontology.org/format_1910 - cmd: null input: - data: term: DNA sequence uri: http://edamontology.org/data_3494 format: - term: FASTQ uri: http://edamontology.org/format_1930 note: null operation: - term: Sequence merging uri: http://edamontology.org/operation_0232 output: - data: term: DNA sequence uri: http://edamontology.org/data_3494 format: - term: FASTQ uri: http://edamontology.org/format_1930 - cmd: null input: - data: term: DNA sequence uri: http://edamontology.org/data_3494 format: - term: FASTQ uri: http://edamontology.org/format_1930 note: null operation: - term: Global alignment uri: http://edamontology.org/operation_0496 output: - data: term: Nucleic acid sequence alignment uri: http://edamontology.org/data_1383 format: - term: SAM uri: http://edamontology.org/format_2573 homepage: http://galaxy.cloud.ba.infn.it:8080/root homepage_status: 0 language: - Python - Bash lastUpdate: '2024-03-25T22:49:35.493467Z' license: Not licensed link: [] maturity: Emerging name: BioMaS (Bioinformatic analysis of Metagenomic amplicons) operatingSystem: - Linux - Mac - Windows otherID: [] owner: bfosso publication: - doi: 10.1186/s12859-015-0595-z metadata: abstract: 'Background: Substantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial communities in any environmental niche. If the investigation is aimed only at the microbiome taxonomic structure, a target-based metagenomic approach, here also referred as Meta-barcoding, is generally applied. This approach commonly involves the selective amplification of a species-specific genetic marker (DNA meta-barcode) in the whole taxonomic range of interest and the exploration of its taxon-related variants through High-Throughput Sequencing (HTS) technologies. The accessibility to proper computational systems for the large-scale bioinformatic analysis of HTS data represents, currently, one of the major challenges in advanced Meta-barcoding projects. Results: BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a new bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data upload and cleaning to final taxonomic identification, that are absolutely required in an appropriately designed Meta-barcoding HTS-based experiment. In its current version, BioMaS allows the analysis of both bacterial and fungal environments starting directly from the raw sequencing data from either Roche 454 or Illumina HTS platforms, following two alternative paths, respectively. BioMaS is implemented into a public web service available at https://recasgateway.ba.infn.it/ and is also available in Galaxy at http://galaxy.cloud.ba.infn.it:8080 (only for Illumina data). Conclusion: BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills. A comparative benchmark, carried out by using a simulated dataset suitably designed to broadly represent the currently known bacterial and fungal world, showed that BioMaS outperforms QIIME and MOTHUR in terms of extent and accuracy of deep taxonomic sequence assignments.' authors: - name: Fosso B. - name: Santamaria M. - name: Marzano M. - name: Alonso-Alemany D. - name: Valiente G. - name: Donvito G. - name: Monaco A. - name: Notarangelo P. - name: Pesole G. citationCount: 45 date: '2015-12-12T00:00:00Z' journal: BMC Bioinformatics title: 'BioMaS: A modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS' note: null pmcid: PMC4486701 pmid: '26130132' type: - Method version: null relation: [] toolType: - Web application topic: - term: Omics uri: http://edamontology.org/topic_3391 validated: 0 version: - '1.0' - accessibility: Open access additionDate: '2016-12-19T14:21:54Z' biotoolsCURIE: biotools:plasmidspades biotoolsID: plasmidspades collectionID: - galaxyPasteur - SPAdes community: null confidence_flag: null cost: null credit: - email: galaxy@pasteur.fr fundrefid: null gridid: null name: Galaxy Support Team note: null orcidid: null rorid: null typeEntity: Person typeRole: - Primary contact url: null description: Genome assembler for plasmids. documentation: - note: null type: - General url: http://spades.bioinf.spbau.ru/release3.11.1/manual.html#plasmid download: [] editPermission: authors: [] type: public elixirCommunity: [] elixirNode: [] elixirPlatform: [] elixir_badge: 0 function: - cmd: null input: - data: term: Data uri: http://edamontology.org/data_0006 format: - term: FASTQ uri: http://edamontology.org/format_1930 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: FASTQ uri: http://edamontology.org/format_1930 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: FASTQ uri: http://edamontology.org/format_1930 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: FASTQ uri: http://edamontology.org/format_1930 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: FASTQ uri: http://edamontology.org/format_1930 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: FASTQ uri: http://edamontology.org/format_1930 - data: term: Sequence alignment uri: http://edamontology.org/data_0863 format: - term: FASTA uri: http://edamontology.org/format_1929 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: FASTQ uri: http://edamontology.org/format_1930 - data: term: Sequence alignment uri: http://edamontology.org/data_0863 format: - term: FASTA uri: http://edamontology.org/format_1929 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: FASTQ uri: http://edamontology.org/format_1930 - data: term: Sequence alignment uri: http://edamontology.org/data_0863 format: - term: FASTA uri: http://edamontology.org/format_1929 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: FASTQ uri: http://edamontology.org/format_1930 note: null operation: - term: Genome assembly uri: http://edamontology.org/operation_0525 output: - data: term: Sequence alignment uri: http://edamontology.org/data_0863 format: - term: FASTA uri: http://edamontology.org/format_1929 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: TSV uri: http://edamontology.org/format_3475 - data: term: Sequence alignment uri: http://edamontology.org/data_0863 format: - term: FASTA uri: http://edamontology.org/format_1929 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: TSV uri: http://edamontology.org/format_3475 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: Textual format uri: http://edamontology.org/format_2330 homepage: http://cab.spbu.ru/software/spades/ homepage_status: 0 language: [] lastUpdate: '2024-03-08T15:31:26.158238Z' license: null link: - note: null type: - Galaxy service url: https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/plasmidspades/plasmidspades/3.9.0 maturity: Mature name: plasmidspades operatingSystem: - Linux - Windows - Mac otherID: [] owner: hmenager publication: - doi: 10.1089/cmb.2012.0021 metadata: abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software. © Copyright 2012, Mary Ann Liebert, Inc. authors: - name: Bankevich A. - name: Nurk S. - name: Antipov D. - name: Gurevich A.A. - name: Dvorkin M. - name: Kulikov A.S. - name: Lesin V.M. - name: Nikolenko S.I. - name: Pham S. - name: Prjibelski A.D. - name: Pyshkin A.V. - name: Sirotkin A.V. - name: Vyahhi N. - name: Tesler G. - name: Alekseyev M.A. - name: Pevzner P.A. citationCount: 15962 date: '2012-05-01T00:00:00Z' journal: Journal of Computational Biology title: 'SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing' note: null pmcid: null pmid: null type: - Primary version: null - doi: 10.1093/nar/gkw343 metadata: 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. 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. citationCount: 1348 date: '2016-07-08T00:00:00Z' journal: Nucleic Acids Research title: 'The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update' note: null pmcid: null pmid: null type: - Other version: null - doi: 10.7490/f1000research.1114334.1 metadata: null note: null pmcid: null pmid: null type: - Other version: null relation: [] toolType: - Web application topic: - term: Sequence assembly uri: http://edamontology.org/topic_0196 - term: Genomics uri: http://edamontology.org/topic_0622 validated: 1 version: - 3.9.0 - accessibility: Open access additionDate: '2016-12-19T14:26:53Z' biotoolsCURIE: biotools:rnaspades biotoolsID: rnaspades collectionID: - galaxyPasteur - SPAdes community: null confidence_flag: null cost: null credit: - email: galaxy@pasteur.fr fundrefid: null gridid: null name: Galaxy Support Team note: null orcidid: null rorid: null typeEntity: Person typeRole: - Primary contact url: null description: Pipeline for de novo transcriptome assembly from RNA-Seq. documentation: - note: null type: - User manual url: http://spades.bioinf.spbau.ru/release3.11.1/rnaspades_manual.html download: [] editPermission: authors: [] type: public elixirCommunity: [] elixirNode: [] elixirPlatform: [] elixir_badge: 0 function: - cmd: null input: - data: term: Data uri: http://edamontology.org/data_0006 format: - term: FASTQ uri: http://edamontology.org/format_1930 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: FASTQ uri: http://edamontology.org/format_1930 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: FASTQ uri: http://edamontology.org/format_1930 note: null operation: - term: De-novo assembly uri: http://edamontology.org/operation_0524 - term: Transcriptome assembly uri: http://edamontology.org/operation_3258 output: - data: term: Sequence alignment uri: http://edamontology.org/data_0863 format: - term: FASTA uri: http://edamontology.org/format_1929 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: Textual format uri: http://edamontology.org/format_2330 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: Textual format uri: http://edamontology.org/format_2330 homepage: http://cab.spbu.ru/software/spades/ homepage_status: 0 language: [] lastUpdate: '2024-03-08T15:29:01.478112Z' license: null link: - note: null type: - Galaxy service url: https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/rnaspades/rnaspades/3.9.0 maturity: Mature name: rnaspades operatingSystem: - Linux - Windows - Mac otherID: - type: rrid value: RRID:SCR_016992 version: null owner: hmenager publication: - doi: 10.1089/cmb.2012.0021 metadata: abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software. © Copyright 2012, Mary Ann Liebert, Inc. authors: - name: Bankevich A. - name: Nurk S. - name: Antipov D. - name: Gurevich A.A. - name: Dvorkin M. - name: Kulikov A.S. - name: Lesin V.M. - name: Nikolenko S.I. - name: Pham S. - name: Prjibelski A.D. - name: Pyshkin A.V. - name: Sirotkin A.V. - name: Vyahhi N. - name: Tesler G. - name: Alekseyev M.A. - name: Pevzner P.A. citationCount: 15962 date: '2012-05-01T00:00:00Z' journal: Journal of Computational Biology title: 'SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing' note: null pmcid: null pmid: null type: - Primary version: null - doi: 10.1093/nar/gkw343 metadata: 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. 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. citationCount: 1348 date: '2016-07-08T00:00:00Z' journal: Nucleic Acids Research title: 'The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update' note: null pmcid: null pmid: null type: - Other version: null - doi: 10.7490/f1000research.1114334.1 metadata: null note: null pmcid: null pmid: null type: - Other version: null relation: [] toolType: - Web application topic: - term: RNA-Seq uri: http://edamontology.org/topic_3170 - term: Transcriptomics uri: http://edamontology.org/topic_3308 - term: Sequencing uri: http://edamontology.org/topic_3168 validated: 1 version: - 3.9.0 - accessibility: Open access additionDate: '2016-12-19T14:26:26Z' biotoolsCURIE: biotools:metaspades biotoolsID: metaspades collectionID: - galaxyPasteur - SPAdes community: null confidence_flag: null cost: null credit: - email: galaxy@pasteur.fr fundrefid: null gridid: null name: Galaxy Support Team note: null orcidid: null rorid: null typeEntity: Person typeRole: - Primary contact url: null description: Genome assembler for metagenomics datasets. documentation: - note: null type: - User manual url: http://spades.bioinf.spbau.ru/release3.11.1/manual.html download: [] editPermission: authors: [] type: public elixirCommunity: [] elixirNode: [] elixirPlatform: [] elixir_badge: 0 function: - cmd: null input: - data: term: Data uri: http://edamontology.org/data_0006 format: - term: FASTQ uri: http://edamontology.org/format_1930 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: FASTQ uri: http://edamontology.org/format_1930 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: FASTQ uri: http://edamontology.org/format_1930 note: null operation: - term: Genome alignment uri: http://edamontology.org/operation_3182 output: - data: term: Sequence alignment uri: http://edamontology.org/data_0863 format: - term: FASTA uri: http://edamontology.org/format_1929 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: TSV uri: http://edamontology.org/format_3475 - data: term: Sequence alignment uri: http://edamontology.org/data_0863 format: - term: FASTA uri: http://edamontology.org/format_1929 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: TSV uri: http://edamontology.org/format_3475 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: Textual format uri: http://edamontology.org/format_2330 homepage: http://cab.spbu.ru/software/spades/ homepage_status: 0 language: - Python lastUpdate: '2024-03-08T15:26:38.619142Z' license: null link: - note: null type: - Galaxy service url: https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/metaspades/metaspades/3.9.0 maturity: Mature name: metaspades operatingSystem: - Linux - Windows - Mac otherID: [] owner: hmenager publication: - doi: 10.1089/cmb.2012.0021 metadata: abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software. © Copyright 2012, Mary Ann Liebert, Inc. authors: - name: Bankevich A. - name: Nurk S. - name: Antipov D. - name: Gurevich A.A. - name: Dvorkin M. - name: Kulikov A.S. - name: Lesin V.M. - name: Nikolenko S.I. - name: Pham S. - name: Prjibelski A.D. - name: Pyshkin A.V. - name: Sirotkin A.V. - name: Vyahhi N. - name: Tesler G. - name: Alekseyev M.A. - name: Pevzner P.A. citationCount: 15962 date: '2012-05-01T00:00:00Z' journal: Journal of Computational Biology title: 'SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing' note: null pmcid: null pmid: null type: - Primary version: null - doi: 10.1093/nar/gkw343 metadata: 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. 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. citationCount: 1348 date: '2016-07-08T00:00:00Z' journal: Nucleic Acids Research title: 'The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update' note: null pmcid: null pmid: null type: - Other version: null - doi: 10.7490/f1000research.1114334.1 metadata: null note: null pmcid: null pmid: null type: - Other version: null relation: [] toolType: - Web application topic: - term: Metagenomics uri: http://edamontology.org/topic_3174 - term: Sequence analysis uri: http://edamontology.org/topic_0080 validated: 1 version: - 3.9.0 - accessibility: Open access additionDate: '2017-08-20T17:30:35Z' biotoolsCURIE: biotools:spades biotoolsID: spades collectionID: - SPAdes - galaxyPasteur - Animal and Crop Genomics community: null confidence_flag: null cost: null credit: - email: spades.support@cab.spbu.ru fundrefid: null gridid: null name: null note: null orcidid: null rorid: null typeEntity: Person typeRole: - Primary contact url: null description: St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. documentation: - note: null type: - User manual url: http://cab.spbu.ru/files/release3.10.1/manual.html download: [] editPermission: authors: - animalandcropgenomics - alexcorm type: public elixirCommunity: [] elixirNode: [] elixirPlatform: [] elixir_badge: 0 function: - cmd: null input: - data: term: Data uri: http://edamontology.org/data_0006 format: - term: FASTQ uri: http://edamontology.org/format_1930 - data: term: Sequence alignment uri: http://edamontology.org/data_0863 format: - term: FASTA uri: http://edamontology.org/format_1929 note: null operation: - term: Genome assembly uri: http://edamontology.org/operation_0525 output: - data: term: Data uri: http://edamontology.org/data_0006 format: - term: TSV uri: http://edamontology.org/format_3475 - data: term: Sequence alignment uri: http://edamontology.org/data_0863 format: - term: FASTA uri: http://edamontology.org/format_1929 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: TSV uri: http://edamontology.org/format_3475 - data: term: Data uri: http://edamontology.org/data_0006 format: - term: Textual format uri: http://edamontology.org/format_2330 homepage: http://cab.spbu.ru/software/spades/ homepage_status: 0 language: - Python lastUpdate: '2024-03-08T15:11:04.466129Z' license: GPL-2.0 link: - note: null type: - Galaxy service url: https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/spades/spades/3.9.0 maturity: Mature name: SPAdes operatingSystem: - Linux - Mac otherID: [] owner: matus.kalas@uib.no publication: - doi: 10.1089/cmb.2012.0021 metadata: abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software. © Copyright 2012, Mary Ann Liebert, Inc. authors: - name: Bankevich A. - name: Nurk S. - name: Antipov D. - name: Gurevich A.A. - name: Dvorkin M. - name: Kulikov A.S. - name: Lesin V.M. - name: Nikolenko S.I. - name: Pham S. - name: Prjibelski A.D. - name: Pyshkin A.V. - name: Sirotkin A.V. - name: Vyahhi N. - name: Tesler G. - name: Alekseyev M.A. - name: Pevzner P.A. citationCount: 15962 date: '2012-05-01T00:00:00Z' journal: Journal of Computational Biology title: 'SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing' note: null pmcid: null pmid: null type: - Primary version: null - doi: 10.7490/f1000research.1114334.1 metadata: null note: null pmcid: null pmid: null type: - Other version: null relation: [] toolType: - Command-line tool topic: - term: Sequence assembly uri: http://edamontology.org/topic_0196 validated: 1 version: [] - accessibility: null additionDate: '2016-05-24T10:51:12Z' biotoolsCURIE: biotools:ribogalaxy biotoolsID: ribogalaxy collectionID: [] community: null confidence_flag: null cost: Free of charge credit: - email: info@sfi.ie fundrefid: null gridid: null name: Science Foundation Ireland note: null orcidid: null rorid: null typeEntity: Funding agency typeRole: - Contributor url: null - email: null fundrefid: null gridid: null name: ucc.ie note: null orcidid: null rorid: null typeEntity: Institute typeRole: - Provider url: http://www.ucc.ie - email: ribogalaxy@gmail.com fundrefid: null gridid: null name: null note: null orcidid: null rorid: null typeEntity: Person typeRole: - Primary contact url: http://ribogalaxy.ucc.ie/ - email: p.baranov@ucc.ie fundrefid: null gridid: null name: Pavel V. Baranov note: null orcidid: null rorid: null typeEntity: null typeRole: [] url: null description: Galaxy-based web server where researchers can pre-process, align, analyze and visualize their own ribosome profiling (ribo-seq) data. GUI-based tools are provided to determine the strength of the triplet periodicity signal in ribo-seq data, generate metagene and ribosome profiles and carry out differential translation expression analysis using the riboSeqR suite. The RUST suite of tools can be used to quickly characterize ribosome profiling datasets to assess their quality and more. documentation: - note: null type: - Terms of use url: http://ribogalaxy.ucc.ie/static/conditions_of_use.html - note: null type: - General url: http://ribogalaxy.ucc.ie/ download: [] editPermission: authors: [] type: private elixirCommunity: - Galaxy elixirNode: [] elixirPlatform: [] elixir_badge: 0 function: - cmd: null input: - data: term: Raw sequence uri: http://edamontology.org/data_0848 format: - term: FASTQ-sanger uri: http://edamontology.org/format_1932 note: Raw ribo-seq and mRNA-seq FASTQ files There are multiple outputs depending on the tool/jobs that are run. Most of the ribo-seq analysis tools provide the output in both spreadsheet and/or visual format. operation: - term: Visualisation uri: http://edamontology.org/operation_0337 - term: Alignment uri: http://edamontology.org/operation_2928 - term: Gene expression profiling uri: http://edamontology.org/operation_0314 - term: Gene expression analysis uri: http://edamontology.org/operation_2495 output: - data: term: Image uri: http://edamontology.org/data_2968 format: - term: PNG uri: http://edamontology.org/format_3603 - data: term: Sequence alignment uri: http://edamontology.org/data_0863 format: - term: BAM uri: http://edamontology.org/format_2572 - term: bigWig uri: http://edamontology.org/format_3006 - data: term: Sequence image uri: http://edamontology.org/data_2969 format: - term: PNG uri: http://edamontology.org/format_3603 homepage: http://ribogalaxy.ucc.ie homepage_status: 0 language: [] lastUpdate: '2024-02-23T09:02:01.891026Z' license: null link: - note: null type: - Repository url: https://github.com/riboseqorg/RiboGalaxy maturity: Mature name: RiboGalaxy operatingSystem: - Windows - Mac otherID: [] owner: A.Michel@ucc.ie publication: - doi: 10.1080/15476286.2016.1141862 metadata: abstract: Ribosome profiling (ribo-seq) is a technique that uses high-throughput sequencing to reveal the exact locations and densities of translating ribosomes at the entire transcriptome level. The technique has become very popular since its inception in 2009. Yet experimentalists who generate ribo-seq data often have to rely on bioinformaticians to process and analyze their data. We present RiboGalaxy (http://ribogalaxy.ucc.ie), a freely available Galaxy-based web server for processing and analyzing ribosome profiling data with the visualization functionality provided by GWIPS-viz (http://gwips.ucc.ie). RiboGalaxy offers researchers a suite of tools specifically tailored for processing ribo-seq and corresponding mRNA-seq data. Researchers can take advantage of the published workflows which reduce the multi-step alignment process to a minimum of inputs from the user. Users can then explore their own aligned data as custom tracks in GWIPS-viz and compare their ribosome profiles to existing ribo-seq tracks from published studies. In addition, users can assess the quality of their ribo-seq data, determine the strength of the triplet periodicity signal, generate meta-gene ribosome profiles as well as analyze the relative impact of mRNA sequence features on local read density. RiboGalaxy is accompanied by extensive documentation and tips for helping users. In addition we provide a forum (http://gwips.ucc.ie/Forum) where we encourage users to post their questions and feedback to improve the overall RiboGalaxy service. authors: - name: Michel A.M. - name: Mullan J.P.A. - name: Velayudhan V. - name: O'Connor P.B.F. - name: Donohue C.A. - name: Baranov P.V. citationCount: 67 date: '2016-03-03T00:00:00Z' journal: RNA Biology title: 'RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data' note: null pmcid: PMC4829337 pmid: '26821742' type: - Primary version: null - doi: 10.1016/J.JMB.2023.168043 metadata: abstract: Ribosome profiling (Ribo-Seq) captures a “snapshot” of ribosomes’ locations at the entire transcriptome of a cell at sub-codon resolution providing insights into gene expression and enabling the discovery of novel translated regions. RiboGalaxy (https://ribogalaxy.genomicsdatascience.ie/), a Galaxy-based platform for processing Ribo-Seq data is a RiboSeq.Org (https://riboseq.org/) resource. RiboSeq.Org is an online gateway to a set of integrated tools for the processing and analysis of Ribo-Seq data. In this RiboGalaxy update we introduce changes to both the tools available on RiboGalaxy and to how the resource is managed on the backend. For example, in order to improve interoperability between Riboseq.Org resources, we added tools that link RiboGalaxy outputs with Trips-Viz and GWIPS-viz browsers for downstream analysis and visualisation. RiboGalaxy's backend now utilises Ansible configuration management which enhances its stability and jobs are executed within Singularity containers and are managed by Slurm, strengthening reproducibility and performance respectively. authors: - name: Fedorova A.D. - name: Tierney J.A.S. - name: Michel A.M. - name: Baranov P.V. citationCount: 1 date: '2023-07-15T00:00:00Z' journal: Journal of Molecular Biology title: 'RiboGalaxy: A Galaxy-based Web Platform for Ribosome Profiling Data Processing – 2023 Update' note: null pmcid: null pmid: '37356899' type: - Review version: null relation: [] toolType: - Workbench topic: - term: Gene expression uri: http://edamontology.org/topic_0203 validated: 1 version: - '1' - accessibility: null additionDate: '2022-11-03T15:52:41.693905Z' biotoolsCURIE: biotools:hmmer_hmmscan_ebi biotoolsID: hmmer_hmmscan_ebi collectionID: - EBI Tools - Job Dispatcher Tools community: null confidence_flag: null cost: null credit: - email: null fundrefid: null gridid: null name: Sean Eddy note: null orcidid: null rorid: null typeEntity: Person typeRole: - Developer url: null - email: null fundrefid: null gridid: null name: EMBL-EBI note: null orcidid: null rorid: null typeEntity: Institute typeRole: - Provider url: null - email: null fundrefid: null gridid: null name: Job Dispatcher note: null orcidid: null rorid: null typeEntity: Project typeRole: - Primary contact url: https://www.ebi.ac.uk/jdispatcher description: HMMER3 hmmscan is used to search sequences against collections of profiles. documentation: - note: null type: - Terms of use url: http://www.ebi.ac.uk/about/terms-of-use - note: null type: - General url: https://www.ebi.ac.uk/jdispatcher/help - note: null type: - General url: http://hmmer.org/ download: - note: null type: Downloads page url: http://hmmer.org/ version: null editPermission: authors: [] type: private elixirCommunity: [] elixirNode: [] elixirPlatform: [] elixir_badge: 0 function: - cmd: null input: - data: term: Sequence record uri: http://edamontology.org/data_0849 format: [] - data: term: Hidden Markov model uri: http://edamontology.org/data_1364 format: [] note: null operation: - term: Sequence database search uri: http://edamontology.org/operation_0338 output: - data: term: Sequence alignment uri: http://edamontology.org/data_0863 format: - term: Database hits (sequence) format uri: http://edamontology.org/format_2066 - data: term: Sequence search results uri: http://edamontology.org/data_0857 format: [] homepage: https://www.ebi.ac.uk/jdispatcher/pfa/hmmer3_hmmscan homepage_status: 0 language: [] lastUpdate: '2024-02-08T10:58:38.007948Z' license: null link: - note: null type: - Helpdesk url: https://www.ebi.ac.uk/about/contact/support/job-dispatcher-services maturity: null name: HMMER hmmscan (EBI) operatingSystem: - Mac - Linux - Windows otherID: [] owner: jdispatcher publication: - doi: 10.1093/nar/gkr367 metadata: abstract: HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. It is now feasible to make efficient profile hidden Markov model (profile HMM) searches via the web. A HMMER web server (http://hmmer.janelia.org) has been designed and implemented such that most protein database searches return within a few seconds. Methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database, and for searching a protein sequence against Pfam. The web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once. All search methods are also available as RESTful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows. We have focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them. © 2011 The Author(s). authors: - name: Finn R.D. - name: Clements J. - name: Eddy S.R. citationCount: 3538 date: '2011-07-01T00:00:00Z' journal: Nucleic Acids Research title: 'HMMER web server: Interactive sequence similarity searching' note: null pmcid: null pmid: null type: - Primary version: null - doi: 10.1093/nar/gkac240 metadata: abstract: The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic. authors: - name: Madeira F. - name: Pearce M. - name: Tivey A.R.N. - name: Basutkar P. - name: Lee J. - name: Edbali O. - name: Madhusoodanan N. - name: Kolesnikov A. - name: Lopez R. citationCount: 699 date: '2022-07-05T00:00:00Z' journal: Nucleic Acids Research title: Search and sequence analysis tools services from EMBL-EBI in 2022 note: null pmcid: null pmid: null type: - Other version: null relation: - biotoolsID: hmmer3 type: uses toolType: - Web application - Web service topic: - term: Sequence analysis uri: http://edamontology.org/topic_0080 - term: Sequence sites, features and motifs uri: http://edamontology.org/topic_0160 - term: Gene and protein families uri: http://edamontology.org/topic_0623 validated: 0 version: - '1' - accessibility: null additionDate: '2022-11-03T15:52:37.739953Z' biotoolsCURIE: biotools:hmmer_phmmer_ebi biotoolsID: hmmer_phmmer_ebi collectionID: - EBI Tools - Job Dispatcher Tools community: null confidence_flag: null cost: null credit: - email: null fundrefid: null gridid: null name: Sean Eddy note: null orcidid: null rorid: null typeEntity: Person typeRole: - Developer url: null - email: null fundrefid: null gridid: null name: EMBL-EBI note: null orcidid: null rorid: null typeEntity: Institute typeRole: - Provider url: null - email: null fundrefid: null gridid: null name: Job Dispatcher note: null orcidid: null rorid: null typeEntity: Project typeRole: - Primary contact url: https://www.ebi.ac.uk/jdispatcher description: HMMER3 phmmer is used to search one or more sequences against a sequence database. documentation: - note: null type: - Terms of use url: http://www.ebi.ac.uk/about/terms-of-use - note: null type: - General url: https://www.ebi.ac.uk/jdispatcher/help - note: null type: - General url: http://hmmer.org/ download: - note: null type: Downloads page url: http://hmmer.org/ version: null editPermission: authors: [] type: private elixirCommunity: [] elixirNode: [] elixirPlatform: [] elixir_badge: 0 function: - cmd: null input: - data: term: Sequence record uri: http://edamontology.org/data_0849 format: [] - data: term: Hidden Markov model uri: http://edamontology.org/data_1364 format: [] note: null operation: - term: Sequence database search uri: http://edamontology.org/operation_0338 output: - data: term: Sequence alignment uri: http://edamontology.org/data_0863 format: - term: Database hits (sequence) format uri: http://edamontology.org/format_2066 - data: term: Sequence search results uri: http://edamontology.org/data_0857 format: [] homepage: https://www.ebi.ac.uk/jdispatcher/pfa/hmmer3_phmmer homepage_status: 0 language: [] lastUpdate: '2024-02-08T10:54:28.651795Z' license: null link: - note: null type: - Helpdesk url: https://www.ebi.ac.uk/about/contact/support/job-dispatcher-services maturity: null name: HMMER phmmer (EBI) operatingSystem: - Mac - Linux - Windows otherID: [] owner: jdispatcher publication: - doi: 10.1093/nar/gkr367 metadata: abstract: HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. It is now feasible to make efficient profile hidden Markov model (profile HMM) searches via the web. A HMMER web server (http://hmmer.janelia.org) has been designed and implemented such that most protein database searches return within a few seconds. Methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database, and for searching a protein sequence against Pfam. The web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once. All search methods are also available as RESTful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows. We have focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them. © 2011 The Author(s). authors: - name: Finn R.D. - name: Clements J. - name: Eddy S.R. citationCount: 3538 date: '2011-07-01T00:00:00Z' journal: Nucleic Acids Research title: 'HMMER web server: Interactive sequence similarity searching' note: null pmcid: null pmid: null type: - Primary version: null - doi: 10.1093/nar/gkac240 metadata: abstract: The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic. authors: - name: Madeira F. - name: Pearce M. - name: Tivey A.R.N. - name: Basutkar P. - name: Lee J. - name: Edbali O. - name: Madhusoodanan N. - name: Kolesnikov A. - name: Lopez R. citationCount: 699 date: '2022-07-05T00:00:00Z' journal: Nucleic Acids Research title: Search and sequence analysis tools services from EMBL-EBI in 2022 note: null pmcid: null pmid: null type: - Other version: null relation: - biotoolsID: hmmer3 type: uses toolType: - Web application - Web service topic: - term: Sequence analysis uri: http://edamontology.org/topic_0080 - term: Sequence sites, features and motifs uri: http://edamontology.org/topic_0160 - term: Gene and protein families uri: http://edamontology.org/topic_0623 validated: 0 version: - '1' - accessibility: null additionDate: '2015-01-29T15:46:55Z' biotoolsCURIE: biotools:seqret-ebi biotoolsID: seqret-ebi collectionID: - EMBOSS at EBI Tools - EBI Tools - Job Dispatcher Tools community: null confidence_flag: null cost: null credit: - email: null fundrefid: null gridid: null name: EMBOSS note: null orcidid: null rorid: null typeEntity: Person typeRole: - Developer url: null - email: null fundrefid: null gridid: null name: EMBL-EBI note: null orcidid: null rorid: null typeEntity: Institute typeRole: - Provider url: null - email: null fundrefid: null gridid: null name: Job Dispatcher note: null orcidid: null rorid: null typeEntity: Project typeRole: - Primary contact url: https://www.ebi.ac.uk/jdispatcher description: Sequence format coversion tool. documentation: - note: null type: - Terms of use url: http://www.ebi.ac.uk/about/terms-of-use - note: null type: - General url: https://www.ebi.ac.uk/jdispatcher/help - note: null type: - General url: https://emboss.sourceforge.net/ download: - note: null type: Downloads page url: https://emboss.sourceforge.net/ version: null editPermission: authors: - biomadeira - nandana type: group elixirCommunity: [] elixirNode: [] elixirPlatform: [] elixir_badge: 0 function: - cmd: null input: - data: term: Sequence uri: http://edamontology.org/data_2044 format: [] - data: term: Sequence alignment uri: http://edamontology.org/data_0863 format: [] note: null operation: - term: Data retrieval uri: http://edamontology.org/operation_2422 - term: Formatting uri: http://edamontology.org/operation_0335 output: - data: term: Sequence uri: http://edamontology.org/data_2044 format: [] - data: term: Sequence alignment uri: http://edamontology.org/data_0863 format: [] homepage: https://www.ebi.ac.uk/jdispatcher/sfc/emboss_seqret homepage_status: 0 language: [] lastUpdate: '2024-02-05T19:37:50.317443Z' license: null link: - note: null type: - Helpdesk url: https://www.ebi.ac.uk/about/contact/support/job-dispatcher-services maturity: null name: seqret (EBI) operatingSystem: - Linux - Windows - Mac otherID: [] owner: jdispatcher publication: - doi: 10.1016/S0168-9525(00)02024-2 metadata: abstract: '' authors: - name: Rice P. - name: Longden L. - name: Bleasby A. citationCount: 6810 date: '2000-06-01T00:00:00Z' journal: Trends in Genetics title: 'EMBOSS: The European Molecular Biology Open Software Suite' note: null pmcid: null pmid: null type: - Primary version: null - doi: 10.1093/nar/gkac240 metadata: null note: null pmcid: null pmid: null type: - Other version: null relation: - biotoolsID: seqret type: uses toolType: - Web application - Web service topic: - term: Data management uri: http://edamontology.org/topic_3071 validated: 1 version: - '1' - accessibility: null additionDate: '2015-01-29T15:47:35Z' biotoolsCURIE: biotools:water-ebi biotoolsID: water-ebi collectionID: - EMBOSS at EBI Tools - EBI Tools - Job Dispatcher Tools community: null confidence_flag: null cost: null credit: - email: null fundrefid: null gridid: null name: EMBOSS note: null orcidid: null rorid: null typeEntity: Person typeRole: - Developer url: null - email: null fundrefid: null gridid: null name: EMBL-EBI note: null orcidid: null rorid: null typeEntity: Institute typeRole: - Provider url: null - email: null fundrefid: null gridid: null name: Job Dispatcher note: null orcidid: null rorid: null typeEntity: Project typeRole: - Primary contact url: https://www.ebi.ac.uk/jdispatcher description: Smith-Waterman local pairwise alignment of sequences. documentation: - note: null type: - Terms of use url: http://www.ebi.ac.uk/about/terms-of-use - note: null type: - General url: https://www.ebi.ac.uk/jdispatcher/help - note: null type: - General url: https://emboss.sourceforge.net/ download: - note: null type: Downloads page url: https://emboss.sourceforge.net/ version: null editPermission: authors: - biomadeira - nandana type: group elixirCommunity: [] elixirNode: [] elixirPlatform: [] elixir_badge: 0 function: - cmd: null input: - data: term: Sequence uri: http://edamontology.org/data_2044 format: [] note: null operation: - term: Pairwise sequence alignment uri: http://edamontology.org/operation_0491 - term: Local alignment uri: http://edamontology.org/operation_0495 output: - data: term: Sequence alignment (pair) uri: http://edamontology.org/data_1381 format: [] homepage: https://www.ebi.ac.uk/jdispatcher/psa/emboss_water homepage_status: 0 language: [] lastUpdate: '2024-02-05T19:25:16.108365Z' license: null link: - note: null type: - Helpdesk url: https://www.ebi.ac.uk/about/contact/support/job-dispatcher-services maturity: null name: water (EBI) operatingSystem: - Linux - Windows - Mac otherID: [] owner: jdispatcher publication: - doi: 10.1016/S0168-9525(00)02024-2 metadata: abstract: '' authors: - name: Rice P. - name: Longden L. - name: Bleasby A. citationCount: 6810 date: '2000-06-01T00:00:00Z' journal: Trends in Genetics title: 'EMBOSS: The European Molecular Biology Open Software Suite' note: null pmcid: null pmid: null type: - Primary version: null - doi: 10.1093/nar/gkac240 metadata: abstract: The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic. authors: - name: Madeira F. - name: Pearce M. - name: Tivey A.R.N. - name: Basutkar P. - name: Lee J. - name: Edbali O. - name: Madhusoodanan N. - name: Kolesnikov A. - name: Lopez R. citationCount: 696 date: '2022-07-05T00:00:00Z' journal: Nucleic Acids Research title: Search and sequence analysis tools services from EMBL-EBI in 2022 note: null pmcid: null pmid: null type: - Other version: null relation: - biotoolsID: water type: uses toolType: - Web application - Web service topic: - term: Sequence analysis uri: http://edamontology.org/topic_0080 validated: 1 version: - '1' next: ?page=2 previous: null