{"id":44836034,"url":"https://github.com/grenaud/vgan","last_synced_at":"2026-02-17T01:36:07.294Z","repository":{"id":59981983,"uuid":"540418384","full_name":"grenaud/vgan","owner":"grenaud","description":"Suite of tools for pangenomics built using vg","archived":false,"fork":false,"pushed_at":"2025-07-18T13:13:48.000Z","size":14970,"stargazers_count":23,"open_issues_count":0,"forks_count":4,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-07-18T17:51:25.887Z","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":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/grenaud.png","metadata":{"files":{"readme":"README.md","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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2022-09-23T11:58:33.000Z","updated_at":"2025-07-18T13:13:52.000Z","dependencies_parsed_at":"2024-10-26T19:35:09.948Z","dependency_job_id":"83ac683f-7272-49cc-9ce3-c81a5964c8e2","html_url":"https://github.com/grenaud/vgan","commit_stats":null,"previous_names":[],"tags_count":8,"template":false,"template_full_name":null,"purl":"pkg:github/grenaud/vgan","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/grenaud%2Fvgan","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/grenaud%2Fvgan/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/grenaud%2Fvgan/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/grenaud%2Fvgan/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/grenaud","download_url":"https://codeload.github.com/grenaud/vgan/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/grenaud%2Fvgan/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29529513,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-17T00:57:22.232Z","status":"ssl_error","status_checked_at":"2026-02-17T00:54:25.811Z","response_time":115,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":"2026-02-17T01:36:06.698Z","updated_at":"2026-02-17T01:36:07.286Z","avatar_url":"https://github.com/grenaud.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?styl=flat)](http://bioconda.github.io/recipes/vgan/README.html)\n# vgan\n\nvgan is a suite of tools for pangenomics. We currently support three main subcommands: Haplocart (for modern human mtDNA haplogroup classification), euka (for bilaterian abundance estimation of ancient environmental DNA) and soibean (for species identification and multiple source estimation of filtered bilateria data from ancient environmental DNA). The underlying data structure is the VG graph (see https://github.com/vgteam/vg).\n\nYou can find the complete **installation guide** and detailed **manuals** for each subcommand in our [**wiki**](https://github.com/grenaud/vgan/wiki).\n\n**vgan is supported for use on Linux systems.**\n\n## Release build (recommended)\n\nThe easiest way to run vgan is to download the static binary. \n\n**Step 1**: Download the static binary.\n\nThe list of releases is here: https://github.com/grenaud/vgan/tags. Each release comes with a static binary. Find the URL of the static binary by right-clicking and selecting \"copy link\"\n\n```\nwget [URL TO RELEASE BINARY]\n```\n\nWhere you paste the URL of the binary, copy the executable in a bin/ directory in your home directory:\n\n```\nmkdir -p $HOME/bin/\ncp vgan $HOME/bin/\n```\n\n**Step 2**: Mark the binary executable:\n\n```\nchmod +x $HOME/bin/vgan\n```\n**Step 3**: Create the vgan folder structure:\n```\nmkdir -p $HOME/share/vgan/euka_dir/\nmkdir -p $HOME/share/vgan/hcfiles/\nmkdir -p $HOME/share/vgan/soibean_dir/\nmkdir -p $HOME/share/vgan/damageProfiles/\nmkdir -p $HOME/share/vgan/plottingScripts/\n```\nOnce the folder structure is created, we can download the necessary files. \nFind download instructions as well as detailed manuals for **euka**, **HaploCart**, and **soibean** in our [**wiki**](https://github.com/grenaud/vgan/wiki). \n\n# Support:\n\nvgan is actively supported and maintained.\nIf you discover an issue with the program, please submit a bug report on GitHub or send an email. \n\nContact:\u003cbr\u003e\n\n  Haplocart: jdru@dtu.dk or gabriel.reno@gmail.com \n  euka: n.alexandra.vogel@gmail.com or gabriel.reno@gmail.com\n  soibean: n.alexandra.vogel@gmail.com or gabriel.reno@gmail.com\n\u003cbr\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgrenaud%2Fvgan","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgrenaud%2Fvgan","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgrenaud%2Fvgan/lists"}