{"id":13751929,"url":"https://github.com/lh3/gfatools","last_synced_at":"2025-05-07T13:01:38.463Z","repository":{"id":2120544,"uuid":"169602869","full_name":"lh3/gfatools","owner":"lh3","description":"Tools for manipulating sequence graphs in the GFA and rGFA formats","archived":false,"fork":false,"pushed_at":"2024-02-20T15:29:14.000Z","size":555,"stargazers_count":197,"open_issues_count":17,"forks_count":18,"subscribers_count":16,"default_branch":"master","last_synced_at":"2024-05-08T22:00:55.378Z","etag":null,"topics":["bioinformatics","genome-graph","genomics"],"latest_commit_sha":null,"homepage":"","language":"C","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/lh3.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","contributing":null,"funding":null,"license":null,"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}},"created_at":"2019-02-07T16:27:36.000Z","updated_at":"2024-08-03T09:03:06.845Z","dependencies_parsed_at":"2023-07-05T16:15:17.967Z","dependency_job_id":"1521b473-1233-415f-af11-5d41ad22633f","html_url":"https://github.com/lh3/gfatools","commit_stats":{"total_commits":291,"total_committers":2,"mean_commits":145.5,"dds":"0.0068728522336769515","last_synced_commit":"109f9274aa5710427d0a70ae76fa833c8e13a8c5"},"previous_names":[],"tags_count":6,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lh3%2Fgfatools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lh3%2Fgfatools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lh3%2Fgfatools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lh3%2Fgfatools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lh3","download_url":"https://codeload.github.com/lh3/gfatools/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252883219,"owners_count":21819157,"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":["bioinformatics","genome-graph","genomics"],"created_at":"2024-08-03T09:00:57.194Z","updated_at":"2025-05-07T13:01:38.411Z","avatar_url":"https://github.com/lh3.png","language":"C","funding_links":[],"categories":["A list of software capable of analyzing mainly **eukaryotic** genomes for pangenomics.","Ranked by starred repositories"],"sub_categories":[],"readme":"## Getting Started\n```sh\ngit clone https://github.com/lh3/gfatools\ncd gfatools \u0026\u0026 make\n# Extract a subgraph\n./gfatools view -l MTh4502 -r 1 test/MT.gfa \u003e sub.gfa\n# Convert GFA to segment FASTA\n./gfatools gfa2fa test/MT.gfa \u003e MT-seg.fa\n# Convert rGFA to stable FASTA or BED\n./gfatools gfa2fa -s test/MT.gfa \u003e MT.fa\n./gfatools gfa2bed -m test/MT.gfa \u003e MT.bed\n```\n\n## Introduction\n\ngfatools is a set of tools for manipulating sequence graphs in the GFA or the\n[rGFA][rGFA] format. It has implemented parsing, subgraph and conversion to\nFASTA/BED. More functionality may be added in future.\n\n[rGFA]: https://github.com/lh3/gfatools/blob/master/doc/rGFA.md\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flh3%2Fgfatools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flh3%2Fgfatools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flh3%2Fgfatools/lists"}