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{ "count": 3379, "next": "?page=2", "previous": null, "list": [ { "name": "BCFtools", "description": "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.", "homepage": "http://www.htslib.org/", "biotoolsID": "bcftools", "biotoolsCURIE": "biotools:bcftools", "version": [ "1.0", "1.1", "1.2", "1.3", "1.3.1", "1.4", "1.4.1", "1.5", "1.6", "1.7", "1.8", "1.9", "1.10", "1.10.1", "1.10.2", "1.11", "1.12", "1.13", "1.14", "1.15", "1.15.1", "1.16", "1.17", "1.18", "1.19", "1.20" ], "otherID": [], "relation": [ { "biotoolsID": "htslib", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" }, { "uri": "http://edamontology.org/operation_3227", "term": "Variant calling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_3020", "term": "BCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_3020", "term": "BCF" } ] } ], "note": "Multiple data munging operations.", "cmd": null } ], "toolType": [ "Command-line tool", "Suite" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_3517", "term": "GWAS study" }, { "uri": "http://edamontology.org/topic_3516", "term": "Genotyping experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C" ], "license": "MIT", "collectionID": [ "BCFtools" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/samtools/bcftools", "type": [ "Repository" ], "note": null }, { "url": "http://www.htslib.org/support/#lists", "type": [ "Mailing list" ], "note": null }, { "url": "https://github.com/samtools/bcftools/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "http://www.htslib.org/download/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.htslib.org/doc/bcftools.html", "type": [ "General" ], "note": null }, { "url": "http://www.htslib.org/workflow/#mapping_to_variant", "type": [ "Other" ], "note": "A workflow for BCFtools." } ], "publication": [ { "doi": "10.1093/bioinformatics/btp352", "pmid": "19505943", "pmcid": "PMC2723002", "type": [ "Primary" ], "version": null, "note": "The Sequence Alignment/Map format and SAMtools.", "metadata": { "title": "The Sequence Alignment/Map format and SAMtools", "abstract": "Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAM tools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. © 2009 The Author(s).", "date": "2009-08-01T00:00:00Z", "citationCount": 37126, "authors": [ { "name": "Li H." }, { "name": "Handsaker B." }, { "name": "Wysoker A." }, { "name": "Fennell T." }, { "name": "Ruan J." }, { "name": "Homer N." }, { "name": "Marth G." }, { "name": "Abecasis G." }, { "name": "Durbin R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/gigascience/giab008", "pmid": "33590861", "pmcid": "PMC7931819", "type": [ "Primary" ], "version": null, "note": "Twelve years of SAMtools and BCFtools.", "metadata": { "title": "Twelve years of SAMtools and BCFtools", "abstract": "Background: SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. Findings: The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Conclusion: Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.", "date": "2021-02-01T00:00:00Z", "citationCount": 3084, "authors": [ { "name": "Danecek P." }, { "name": "Bonfield J.K." }, { "name": "Liddle J." }, { "name": "Marshall J." }, { "name": "Ohan V." }, { "name": "Pollard M.O." }, { "name": "Whitwham A." }, { "name": "Keane T." }, { "name": "McCarthy S.A." }, { "name": "Davies R.M." } ], "journal": "GigaScience" } } ], "credit": [ { "name": "Wellcome Sanger Institute", "email": "samtools@sanger.ac.uk", "url": "https://www.sanger.ac.uk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Samtools Help mailing list", "email": null, "url": "https://lists.sourceforge.net/lists/listinfo/samtools-help", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Support" ], "note": null } ], "community": null, "owner": "awhitwham", "additionDate": "2015-08-24T08:35:55Z", "lastUpdate": "2024-04-16T10:25:06.228249Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SAMtools", "description": "SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. 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It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAM tools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. © 2009 The Author(s).", "date": "2009-08-01T00:00:00Z", "citationCount": 37126, "authors": [ { "name": "Li H." }, { "name": "Handsaker B." }, { "name": "Wysoker A." }, { "name": "Fennell T." }, { "name": "Ruan J." }, { "name": "Homer N." }, { "name": "Marth G." }, { "name": "Abecasis G." }, { "name": "Durbin R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/gigascience/giab008", "pmid": "33590861", "pmcid": "PMC7931819", "type": [ "Primary" ], "version": null, "note": "Twelve years of SAMtools and BCFtools.", "metadata": { "title": "Twelve years of SAMtools and BCFtools", "abstract": "Background: SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. Findings: The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Conclusion: Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.", "date": "2021-02-01T00:00:00Z", "citationCount": 3084, "authors": [ { "name": "Danecek P." }, { "name": "Bonfield J.K." }, { "name": "Liddle J." }, { "name": "Marshall J." }, { "name": "Ohan V." }, { "name": "Pollard M.O." }, { "name": "Whitwham A." }, { "name": "Keane T." }, { "name": "McCarthy S.A." }, { "name": "Davies R.M." } ], "journal": "GigaScience" } }, { "doi": "10.1093/bioinformatics/btr509", "pmid": "21903627", "pmcid": "PMC3198575", "type": [], "version": null, "note": null, "metadata": { "title": "A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data", "abstract": "Motivation: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample low-coverage sequencing or somatic mutation discovery). These applications press for the development of new methods for analyzing sequence data with uncertainty. Results: We present a statistical framework for calling SNPs, discovering somatic mutations, inferring population genetical parameters and performing association tests directly based on sequencing data without explicit genotyping or linkage-based imputation. On real data, we demonstrate that our method achieves comparable accuracy to alternative methods for estimating site allele count, for inferring allele frequency spectrum and for association mapping. We also highlight the necessity of using symmetric datasets for finding somatic mutations and confirm that for discovering rare events, mismapping is frequently the leading source of errors. © The Author 2011. Published by Oxford University Press. All rights reserved.", "date": "2011-11-01T00:00:00Z", "citationCount": 3826, "authors": [ { "name": "Li H." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Richard Durbin", "email": "rd@sanger.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Wellcome Sanger Institute", "email": "samtools@sanger.ac.uk", "url": "https://www.sanger.ac.uk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider", "Primary contact" ], "note": null }, { "name": "Samtools Help mailing list", "email": null, "url": "https://lists.sourceforge.net/lists/listinfo/samtools-help", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Support" ], "note": null } ], "community": { "biolib": { "app_name": "samtools", "author_name": "SAMtools", "author_username": "samtools" } }, "owner": "awhitwham", "additionDate": "2017-01-13T13:16:12Z", "lastUpdate": "2024-04-16T10:22:46.809965Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE", "animalandcropgenomics", "alice", "awhitwham", "sergitobara" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HTSlib", "description": "The main purpose of HTSlib is to provide access to genomic information files, both alignment data (SAM, BAM, and CRAM formats) and variant data (VCF and BCF formats). The library also provides interfaces to access and index genome reference data in FASTA format and tab-delimited files with genomic coordinates. It is utilized and incorporated into both SAMtools and BCFtools.", "homepage": "http://www.htslib.org/", "biotoolsID": "htslib", "biotoolsCURIE": "biotools:htslib", "version": [ "1.0", "1.1", "1.2", "1.2.1", "1.3", "1.3.1", "1.3.2", "1.4", "1.4.1", "1.5", "1.6", "1.7", "1.8", "1.9", "1.10", "1.10.1", "1.10.2", "1.11", "1.12", "1.13", "1.14", "1.15", "1.15.1", "1.16", "1.17", "1.18", "1.19", "1.20" ], "otherID": [], "relation": [ { "biotoolsID": "samtools", "type": "usedBy" }, { "biotoolsID": "bcftools", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" }, { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_3462", "term": "CRAM" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_3020", "term": "BCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" }, { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_3462", "term": "CRAM" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_3020", "term": "BCF" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C" ], "license": "MIT", "collectionID": [ "Animal and Crop Genomics" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/samtools/htslib", "type": [ "Repository" ], "note": null }, { "url": "http://www.htslib.org/support/#lists", "type": [ "Mailing list" ], "note": null }, { "url": "https://github.com/samtools/htslib/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "http://www.htslib.org/download/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.htslib.org/doc/#manual-pages", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/gigascience/giab007", "pmid": "33594436", "pmcid": "PMC7931820", "type": [ "Primary" ], "version": null, "note": "HTSlib: C library for reading/writing high-throughput sequencing data.", "metadata": { "title": "HTSlib: C library for reading/writing high-Throughput sequencing data", "abstract": "Background: Since the original publication of the VCF and SAM formats, an explosion of software tools have been created to process these data files. To facilitate this a library was produced out of the original SAMtools implementation, with a focus on performance and robustness. The file formats themselves have become international standards under the jurisdiction of the Global Alliance for Genomics and Health. Findings: We present a software library for providing programmatic access to sequencing alignment and variant formats. It was born out of the widely used SAMtools and BCFtools applications. Considerable improvements have been made to the original code plus many new features including newer access protocols, the addition of the CRAM file format, better indexing and iterators, and better use of threading. Conclusion: Since the original Samtools release, performance has been considerably improved, with a BAM read-write loop running 5 times faster and BAM to SAM conversion 13 times faster (both using 16 threads, compared to Samtools 0.1.19). Widespread adoption has seen HTSlib downloaded >1 million times from GitHub and conda. The C library has been used directly by an estimated 900 GitHub projects and has been incorporated into Perl, Python, Rust, and R, significantly expanding the number of uses via other languages. HTSlib is open source and is freely available from htslib.org under MIT/BSD license.", "date": "2021-02-01T00:00:00Z", "citationCount": 116, "authors": [ { "name": "Bonfield J.K." }, { "name": "Marshall J." }, { "name": "Danecek P." }, { "name": "Li H." }, { "name": "Ohan V." }, { "name": "Whitwham A." }, { "name": "Keane T." } ], "journal": "GigaScience" } } ], "credit": [ { "name": "Wellcome Sanger Institute", "email": "samtools@sanger.ac.uk", "url": "https://www.sanger.ac.uk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider", "Primary contact" ], "note": null }, { "name": "Samtools Help mailing list", "email": null, "url": "https://lists.sourceforge.net/lists/listinfo/samtools-help", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Support" ], "note": null } ], "community": null, "owner": "awhitwham", "additionDate": "2017-08-20T16:07:58Z", "lastUpdate": "2024-04-16T10:19:42.968075Z", "editPermission": { "type": "group", "authors": [ "animalandcropgenomics", "smoe" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "vegan", "description": "Ordination methods, diversity analysis and other functions for community and vegetation ecologists", "homepage": "https://cran.r-project.org/web/packages/vegan/index.html", "biotoolsID": "vegan", "biotoolsCURIE": "biotools:vegan", "version": [ "2.4-3", "2.6-4" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" }, { "uri": "http://edamontology.org/operation_2945", "term": "Analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0610", "term": "Ecology" }, { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" }, { "uri": "http://edamontology.org/topic_3855", "term": "Environmental science" } ], "operatingSystem": [], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "community": null, "owner": "rlibouban", "additionDate": "2024-03-12T14:45:13.869292Z", "lastUpdate": "2024-03-12T14:45:13.871787Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "usher", "description": "The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. 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