{"id":20153562,"url":"https://github.com/seqan/vaquita","last_synced_at":"2025-10-26T02:44:55.212Z","repository":{"id":52193844,"uuid":"81968114","full_name":"seqan/vaquita","owner":"seqan","description":"Identification of structural variations","archived":false,"fork":false,"pushed_at":"2022-07-22T11:23:16.000Z","size":2660,"stargazers_count":12,"open_issues_count":11,"forks_count":4,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-23T23:27:03.240Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/seqan.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.txt","contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2017-02-14T16:58:46.000Z","updated_at":"2021-02-10T11:24:41.000Z","dependencies_parsed_at":"2022-08-27T14:56:13.458Z","dependency_job_id":null,"html_url":"https://github.com/seqan/vaquita","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fvaquita","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fvaquita/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fvaquita/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fvaquita/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/seqan","download_url":"https://codeload.github.com/seqan/vaquita/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248115019,"owners_count":21050154,"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":"2024-11-13T23:19:44.296Z","updated_at":"2025-10-26T02:44:55.151Z","avatar_url":"https://github.com/seqan.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Build Status](https://travis-ci.org/seqan/vaquita.svg?branch=master)](https://travis-ci.org/seqan/vaquita)\n\u003cp align=\"center\"\u003e\u003cimg height=\"200\" src=\"http://jongkyu.kim/images/vaquita_420_340.png\"\u003e\u003c/p\u003e\n\n[Vaquita](http://www.worldwildlife.org/species/vaquita) accurately identifies __structural variations__ using split-reads, discordant read-pairs, soft-clipped reads, and read-depth information. Vaquita does not depend on external tools and very fast. You can analyze __50x WGS sample within an hour__.\n\n\nDownload \u0026 Compile\n-----------------\n    git clone https://github.com/seqan/vaquita.git\n    mkdir vaquita-build \u0026\u0026 cd vaquita-build\n    cmake ../vaquita \u0026\u0026 make vaquita -j 4\n\nVaquita supports `GCC≥4.9` and `Clang≥3.8`.\n\nUsage\n-----------------\n    vaquita call -r [reference.fa] [input.bam] \u003e [output.vcf]\n\nThe `.bam` file must be sorted by coordinate (eg. `samtools sort`).\nYou can find more options using `vaquita call --help`.\n\nCitation\n-----------------\nJongkyu Kim and Knut Reinert, Vaquita: Fast and Accurate Identification of Structural Variations using Combined Evidence. _Workshop on Algorithmic Bioinformatics (WABI) 2017_\n\nDOI: [10.4230/LIPIcs.WABI.2017.13](http://drops.dagstuhl.de/opus/volltexte/2017/7635/)\n\n* You can find all the scripts and information about raw datasets that I used for benchmarking at [this repository](https://github.com/xenigmax/vaquita_WABI2017).\n\nContact\n-----------------\nJongkyu Kim (vaquita@jongkyu.kim)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fseqan%2Fvaquita","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fseqan%2Fvaquita","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fseqan%2Fvaquita/lists"}