{"id":13606315,"url":"https://github.com/samtools/samtools","last_synced_at":"2025-12-29T22:04:38.424Z","repository":{"id":2674885,"uuid":"3666841","full_name":"samtools/samtools","owner":"samtools","description":"Tools (written in C using htslib) for manipulating next-generation sequencing data","archived":false,"fork":false,"pushed_at":"2024-04-24T17:16:55.000Z","size":15347,"stargazers_count":1548,"open_issues_count":187,"forks_count":570,"subscribers_count":101,"default_branch":"develop","last_synced_at":"2024-04-25T15:05:56.787Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://htslib.org/","language":"C","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/samtools.png","metadata":{"files":{"readme":"README","changelog":"ChangeLog.old","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS","dei":null,"publiccode":null,"codemeta":null}},"created_at":"2012-03-09T02:49:58.000Z","updated_at":"2024-04-30T15:49:28.276Z","dependencies_parsed_at":"2023-07-06T07:28:09.701Z","dependency_job_id":"6c878cc7-38dc-4ffd-8c69-eb42b6d4ff3e","html_url":"https://github.com/samtools/samtools","commit_stats":{"total_commits":2391,"total_committers":100,"mean_commits":23.91,"dds":0.7712254286909244,"last_synced_commit":"04d53eba2533eba1fd8090ef448c6628f3d83c81"},"previous_names":[],"tags_count":66,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/samtools%2Fsamtools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/samtools%2Fsamtools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/samtools%2Fsamtools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/samtools%2Fsamtools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/samtools","download_url":"https://codeload.github.com/samtools/samtools/tar.gz/refs/heads/develop","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248539783,"owners_count":21121233,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-08-01T19:01:08.018Z","updated_at":"2025-12-29T22:04:38.418Z","avatar_url":"https://github.com/samtools.png","language":"C","funding_links":[],"categories":["C","Essentials","Suite tools","Ranked by starred repositories"],"sub_categories":["Offline Tools"],"readme":"Samtools implements various utilities for post-processing alignments in the\nSAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction\nwith bcftools), and a simple alignment viewer.\n\n\nBuilding samtools\n=================\n\nThe typical simple case of building Samtools using the HTSlib bundled within\nthis Samtools release tarball is done as follows:\n\n    cd .../samtools-1.23 # Within the unpacked release directory\n    ./configure\n    make\n\nYou may wish to copy the resulting samtools executable into somewhere on your\n$PATH, or run it where it is.\n\nRather than running-in-place like that, the next simplest typical case is to\ninstall samtools etc properly into a directory of your choosing.  Building for\ninstallation using the HTSlib bundled within this Samtools release tarball,\nand building the various HTSlib utilities such as bgzip is done as follows:\n\n    cd .../samtools-1.23 # Within the unpacked release directory\n    ./configure --prefix=/path/to/location\n    make all all-htslib\n    make install install-htslib\n\nYou will likely wish to add /path/to/location/bin to your $PATH.\n\nSee INSTALL for full building and installation instructions and details.\n\nBuilding with HTSlib plug-in support\n====================================\n\nEnabling plug-ins causes some parts of HTSlib to be built as separate modules.\nThere are two advantages to this:\n\n * The static library libhts.a has fewer dependencies, which makes linking\n   third-party code against it easier.\n\n * It is possible to build extra plug-ins in addition to the ones that are\n   bundled with HTSlib.  For example, the hts-plugins repository\n   \u003chttps://github.com/samtools/htslib-plugins\u003e includes a module that\n   allows direct access to files stored in an iRODS data management\n   repository (see \u003chttps://irods.org/\u003e).\n\nTo build with plug-ins, you need to use the --enable-plugins configure option\nas follows:\n\n    cd .../samtools-1.23 # Within the unpacked release directory\n    ./configure --enable-plugins --prefix=/path/to/location\n    make all all-htslib\n    make install install-htslib\n\nThere are two other configure options that affect plug-ins.  These are:\n   --with-plugin-dir=DIR     plug-in installation location\n   --with-plugin-path=PATH   default plug-in search path\n\nThe default for --with-plugin-dir is \u003cprefix\u003e/libexec/htslib.\n--with-plugin-path sets the built-in search path used to find the plug-ins.  By\ndefault this is the directory set by the --with-plugin-dir option.  Multiple\ndirectories should be separated by colons.\n\nSetting --with-plugin-path is useful if you want to run directly from\nthe source distribution instead of installing the package.  In that case\nyou can use:\n\n    cd .../samtools-1.23 # Within the unpacked release directory\n    ./configure --enable-plugins --with-plugin-path=$PWD/htslib-1.23\n    make all all-htslib\n\nIt is possible to override the built-in search path using the HTS_PATH\nenvironment variable.  Directories should be separated by colons.  To\ninclude the built-in path, add an empty entry to HTS_PATH:\n\n   export HTS_PATH=:/my/path            # Search built-in path first\n   export HTS_PATH=/my/path:            # Search built-in path last\n   export HTS_PATH=/my/path1::/my/path2 # Search built-in path between others\n\nUsing an optimised zlib library\n===============================\n\nSamtools has been minimally tested against both the Intel-optimised and\nCloudFlare-optimised zlibs and shown to work.\n\nThey can be downloaded from:\n\n    https://github.com/jtkukunas/zlib     # Intel\n    https://github.com/cloudflare/zlib    # CloudFlare\n\nNeither Samtools nor HTSlib needs recompiling to use these optimised libraries,\nbut the LD_LIBRARY_PATH environment variable should be set to a directory\ncontaining the libz.so.1 file.\n\nBenchmarks comparing the various zlibs are available at:\n\n    http://www.htslib.org/benchmarks/zlib.html\n\nIt is recommended that you perform your own rigorous tests for an entire\npipeline if you wish to switch to one of the optimised zlib implementations.\n\nCiting\n======\n\nPlease cite this paper when using SAMtools for your publications:\n\nTwelve years of SAMtools and BCFtools\nPetr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li\nGigaScience, Volume 10, Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008\n\n@article{10.1093/gigascience/giab008,\n    author = {Danecek, Petr and Bonfield, James K and Liddle, Jennifer and Marshall, John and Ohan, Valeriu and Pollard, Martin O and Whitwham, Andrew and Keane, Thomas and McCarthy, Shane A and Davies, Robert M and Li, Heng},\n    title = \"{Twelve years of SAMtools and BCFtools}\",\n    journal = {GigaScience},\n    volume = {10},\n    number = {2},\n    year = {2021},\n    month = {02},\n    abstract = \"{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.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.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 \\\\\u0026gt;1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.}\",\n    issn = {2047-217X},\n    doi = {10.1093/gigascience/giab008},\n    url = {https://doi.org/10.1093/gigascience/giab008},\n    note = {giab008},\n    eprint = {https://academic.oup.com/gigascience/article-pdf/10/2/giab008/36332246/giab008.pdf},\n}\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsamtools%2Fsamtools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsamtools%2Fsamtools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsamtools%2Fsamtools/lists"}