{"id":13703934,"url":"https://github.com/bbuchfink/diamond","last_synced_at":"2025-05-14T16:14:10.541Z","repository":{"id":28471192,"uuid":"31987083","full_name":"bbuchfink/diamond","owner":"bbuchfink","description":"Accelerated BLAST compatible local sequence aligner.","archived":false,"fork":false,"pushed_at":"2025-03-16T18:55:21.000Z","size":32808,"stargazers_count":1126,"open_issues_count":190,"forks_count":181,"subscribers_count":36,"default_branch":"master","last_synced_at":"2025-04-13T01:56:33.985Z","etag":null,"topics":["sequence-alignment"],"latest_commit_sha":null,"homepage":"","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/bbuchfink.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2015-03-10T23:19:00.000Z","updated_at":"2025-04-09T05:26:25.000Z","dependencies_parsed_at":"2024-11-14T21:20:17.824Z","dependency_job_id":"fa291356-680e-4c54-8b89-7f0bce348242","html_url":"https://github.com/bbuchfink/diamond","commit_stats":{"total_commits":1887,"total_committers":25,"mean_commits":75.48,"dds":0.09379968203497613,"last_synced_commit":"a77eaa448c0a38dce5d1a840b13b15d8d792f150"},"previous_names":[],"tags_count":114,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bbuchfink%2Fdiamond","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bbuchfink%2Fdiamond/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bbuchfink%2Fdiamond/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bbuchfink%2Fdiamond/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bbuchfink","download_url":"https://codeload.github.com/bbuchfink/diamond/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248654050,"owners_count":21140235,"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":["sequence-alignment"],"created_at":"2024-08-02T21:01:01.922Z","updated_at":"2025-04-13T01:57:04.547Z","avatar_url":"https://github.com/bbuchfink.png","language":"C++","funding_links":[],"categories":["Next Generation Sequencing","C++","Top Packages by Category"],"sub_categories":["Sequence Alignment","Virus and Phage Identification"],"readme":"![diamond](http://www.diamondsearch.org/diamond_white_95px.png)\n\nIntroduction\n============\n\nDIAMOND is a sequence aligner for protein and translated DNA searches,\ndesigned for high performance analysis of big sequence data. The key\nfeatures are:\n\n-   Pairwise alignment of proteins and translated DNA at 100x-10,000x\n    speed of BLAST.\n-   [Protein clustering of up to tens of billions of proteins](https://github.com/bbuchfink/diamond/wiki/Clustering)\n-   Frameshift alignments for long read analysis.\n-   Low resource requirements and suitable for running on standard\n    desktops or laptops.\n-   Various output formats, including BLAST pairwise, tabular and XML,\n    as well as taxonomic classification.\n\n[![Build](https://github.com/bbuchfink/diamond/actions/workflows/cmake.yml/badge.svg)](https://github.com/bbuchfink/diamond/actions/workflows/cmake.yml)\n[![image](https://img.shields.io/cirrus/github/bbuchfink/diamond)](https://cirrus-ci.com/github/bbuchfink/diamond/master)\n[![image](https://img.shields.io/github/downloads/bbuchfink/diamond/total)](https://github.com/bbuchfink/diamond/releases)\n[![image](https://anaconda.org/bioconda/diamond/badges/version.svg)](https://anaconda.org/bioconda/diamond)\n[![image](https://anaconda.org/bioconda/diamond/badges/downloads.svg)](https://anaconda.org/bioconda/diamond)\n[![image](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fraw.githubusercontent.com%2Fbbuchfink%2Fdiamond-data%2Frefs%2Fheads%2Fmain%2Fcitations.json\u0026query=%24.citations\u0026style=flat\u0026label=Citations\u0026color=%23a020f0\n)](https://scholar.google.com/citations?user=kjPIF1cAAAAJ)\n    \nDocumentation\n=============\nThe online documentation is located at the [GitHub Wiki](https://github.com/bbuchfink/diamond/wiki).\n\nSupport\n=======\nDIAMOND is actively supported and developed software. Please use the [issue tracker](https://github.com/bbuchfink/diamond/issues) for malfunctions and the [GitHub discussions](https://github.com/bbuchfink/diamond/discussions) for questions, comments, feature requests, etc.\n\nAbout\n=====\nDIAMOND is developed by Benjamin Buchfink at the Max Planck Institute for Biology\nTübingen in collaboration with the Drost lab at the University of Dundee. From 2019-2024,\nit was developed by Benjamin Buchfink at the Drost lab, Max Planck Institute for Biology\nTübingen. From 2018-2019, its development was supported by the German Federal Ministry\nfor Economic Affairs and Energy through an EXIST grant. From 2016-2018, it was developed\nby Benjamin Buchfink as an independent researcher. From 2013-2015, the initial version\nwas developed by Benjamin Buchfink at the Huson lab, University of Tübingen, Germany.\n\n\\[[:email:Email](mailto:buchfink@gmail.com)\\]\n\\[[X](https://x.com/bbuchfink)\\]\n\\[[Bluesky](https://bsky.app/profile/bbuchfink.bsky.social)\\]\n\\[[LinkedIn](https://www.linkedin.com/in/benjamin-buchfink-875692105/)\\]\n\\[[Google Scholar](https://scholar.google.de/citations?user=kjPIF1cAAAAJ)\\]\n\\[[Drost lab](https://drostlab.com/)\\]\n\\[[MPI-BIO](https://www.bio.mpg.de/)\\]\n\n**When using the tool in published research, please cite:**\n\n-   Buchfink B, Reuter K, Drost HG, \\\"Sensitive protein alignments at tree-of-life\n    scale using DIAMOND\\\", *Nature Methods* **18**, 366–368 (2021).\n    [doi:10.1038/s41592-021-01101-x](https://doi.org/10.1038/s41592-021-01101-x)\n\nFor sequence clustering:\n\n-   Buchfink B, Ashkenazy H, Reuter K, Kennedy JA, Drost HG, \\\"Sensitive clustering\n    of protein sequences at tree-of-life scale using DIAMOND DeepClust\\\", *bioRxiv*\n    2023.01.24.525373; doi: https://doi.org/10.1101/2023.01.24.525373 \n\nOriginal publication to cite DIAMOND until v0.9.25:\n\n-   Buchfink B, Xie C, Huson DH, \\\"Fast and sensitive protein alignment\n    using DIAMOND\\\", *Nature Methods* **12**, 59-60 (2015).\n    [doi:10.1038/nmeth.3176](https://doi.org/10.1038/nmeth.3176)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbbuchfink%2Fdiamond","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbbuchfink%2Fdiamond","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbbuchfink%2Fdiamond/lists"}