{"id":20792192,"url":"https://github.com/epruesse/sina","last_synced_at":"2025-05-05T21:28:04.758Z","repository":{"id":84873252,"uuid":"76606154","full_name":"epruesse/SINA","owner":"epruesse","description":"SINA - Reference based multiple sequence alignment","archived":false,"fork":false,"pushed_at":"2020-12-13T21:41:05.000Z","size":1426,"stargazers_count":41,"open_issues_count":26,"forks_count":4,"subscribers_count":7,"default_branch":"master","last_synced_at":"2024-11-04T08:03:10.508Z","etag":null,"topics":["16s","alignment","bioinformatics","rrna","sequence","silva"],"latest_commit_sha":null,"homepage":"https://sina.readthedocs.io","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/epruesse.png","metadata":{"files":{"readme":"README.rst","changelog":null,"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}},"created_at":"2016-12-16T00:07:10.000Z","updated_at":"2024-09-26T13:22:41.000Z","dependencies_parsed_at":"2023-03-03T10:30:26.060Z","dependency_job_id":null,"html_url":"https://github.com/epruesse/SINA","commit_stats":null,"previous_names":[],"tags_count":20,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epruesse%2FSINA","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epruesse%2FSINA/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epruesse%2FSINA/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epruesse%2FSINA/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/epruesse","download_url":"https://codeload.github.com/epruesse/SINA/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":225059808,"owners_count":17414750,"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":["16s","alignment","bioinformatics","rrna","sequence","silva"],"created_at":"2024-11-17T15:49:29.676Z","updated_at":"2024-11-17T15:49:30.316Z","avatar_url":"https://github.com/epruesse.png","language":"C++","readme":"SINA - reference based multiple sequence alignment\n==================================================\n\n|latest| |Bioconda| |downloads| |TravisCI| |CircleCI| |Read the Docs| |Codecov|\n\n.. |latest| image:: https://img.shields.io/github/release/epruesse/SINA/all.svg?label=latest\n.. |release| image:: https://img.shields.io/github/release/epruesse/SINA.svg\n.. |Bioconda| image:: https://img.shields.io/conda/vn/Bioconda/sina.svg\n   :target: https://bioconda.github.io/recipes/sina/README.html\n.. |TravisCI| image:: https://img.shields.io/travis/epruesse/SINA.svg?label=build%20(TravisCI)\n   :target: https://travis-ci.org/epruesse/SINA\n.. |CircleCI| image:: https://img.shields.io/circleci/project/github/epruesse/SINA.svg?label=build%20(CircleCI)\n   :target: https://circleci.com/gh/epruesse/SINA\n.. |Codecov| image:: https://img.shields.io/codecov/c/github/epruesse/sina.svg\n   :target: https://codecov.io/gh/epruesse/SINA\n.. |Read the Docs| image:: https://img.shields.io/readthedocs/sina/latest.svg\n   :target: https://readthedocs.org/projects/sina/builds\n.. |downloads| image:: https://img.shields.io/conda/dn/bioconda/sina.svg?style=flat\n\n\nSINA aligns nucleotide sequences to match a pre-existing MSA using\na graph based alignment algorithm similar to PoA. The graph approach\nallows SINA to incorporate information from many reference sequences\nbuilding without blurring highly variable regions. While\npure NAST implementations depend highly on finding a good match in\nthe reference database, SINA is able to align sequences relatively\ndistant to references with good quality and will yield a robust result\nfor query sequences with many close reference.\n\nFeatures\n--------\n\n- Speed. Aligning 100,000 full length rRNA against the SILVA NR takes 40 minutes on a mid-sized 2018 desktop computer. Aligning 1,000,000 V4 amplicons takes about 60 minutes.\n- Accuracy. SINA is used to build the SILVA_ SSU and LSU rRNA databases.\n- Classification. SINA includes an LCA based classification module.\n- ARB. SINA is able to directly read and write ARB_ format files such as distributed by the SILVA_ project.\n\n.. _SILVA: https://www.arb-silva.de\n.. _ARB: https://www.arb-home.de\n\nOnline Version\n--------------\n\nAn online version for submitting small batches of sequences is made\navailable by the SILVA_ project as part of their\n`ACT: Alignment, Classification and Tree Service \u003chttps://www.arb-silva.de/aligner\u003e`_.\nIn addition to SINA's alignment and classification stages, ACT allows directly building\nphylogenetic trees with RAxML or FastTree from your sequences and (optionally)\nadditional sequences chosen using SINA's add-neighbors feature.\n\nInstalling SINA\n---------------\n\nThe preferred way to install SINA locally is via `Bioconda \u003chttps://bioconda.github.io\u003e`_.\nIf you have a working Bioconda installation, just run::\n\n    conda create -n sina sina\n    conda activate sina\n\nAlternatively, self-contained images are available at\nhttps://github.com/epruesse/SINA/releases. Choose the most recent ``tar.gz``\nappropriate for your operating system and unpack::\n\n   tar xf sina-1.7.3-dev-dev-linux.tar.gz\n   cd sina-1.7.3-dev-dev\n   ./sina\n\n\nDocumentation\n-------------\n\nThe full documentation is available at https://sina.readthedocs.io.\n\nThe algorithm is explained in the paper:\n\n  Elmar Pruesse, Jörg Peplies, Frank Oliver Glöckner; *SINA: Accurate\n  high-throughput multiple sequence alignment of ribosomal RNA\n  genes.* Bioinformatics 2012; 28 (14): 1823-1829.\n  `doi:10.1093/bioinformatics/bts252 \u003chttps://doi.org/10.1093/bioinformatics/bts252\u003e`_\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepruesse%2Fsina","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fepruesse%2Fsina","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepruesse%2Fsina/lists"}