{"id":20547461,"url":"https://github.com/ggonnella/rgfa","last_synced_at":"2025-08-30T17:13:00.399Z","repository":{"id":56892182,"uuid":"63710075","full_name":"ggonnella/rgfa","owner":"ggonnella","description":"Ruby library for handling GFA files","archived":false,"fork":false,"pushed_at":"2025-07-10T08:11:25.000Z","size":6626,"stargazers_count":17,"open_issues_count":3,"forks_count":2,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-08-24T12:47:50.203Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Ruby","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/ggonnella.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2016-07-19T16:23:08.000Z","updated_at":"2025-08-06T20:20:36.000Z","dependencies_parsed_at":"2022-08-21T01:20:13.039Z","dependency_job_id":null,"html_url":"https://github.com/ggonnella/rgfa","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/ggonnella/rgfa","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ggonnella%2Frgfa","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ggonnella%2Frgfa/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ggonnella%2Frgfa/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ggonnella%2Frgfa/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ggonnella","download_url":"https://codeload.github.com/ggonnella/rgfa/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ggonnella%2Frgfa/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":272878320,"owners_count":25008336,"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","status":"online","status_checked_at":"2025-08-30T02:00:09.474Z","response_time":77,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":"2024-11-16T02:08:23.930Z","updated_at":"2025-08-30T17:13:00.380Z","avatar_url":"https://github.com/ggonnella.png","language":"Ruby","funding_links":[],"categories":[],"sub_categories":[],"readme":"The Graphical Fragment Assembly (GFA) is a proposed format which allow\nto describe the product of sequence assembly.\nThis gem implements the proposed specifications for the GFA format\ndescribed under https://github.com/GFA-spec/GFA-spec/blob/master/GFA-spec.md\nas close as possible.\n\nThe library allows to create a RGFA object from a file in the GFA format\nor from scratch, to enumerate the graph elements (segments, links,\ncontainments, paths and header lines), to traverse the graph (by\ntraversing all links outgoing from or incoming to a segment), to search for\nelements (e.g. which links connect two segments) and to manipulate the\ngraph (e.g. to eliminate a link or a segment or to duplicate a segment\ndistributing the read counts evenly on the copies).\n\n## Installation\n\nThe latest release of the gem can be installed from the rubygems repository\nusing:\n```gem install rgfa```\n\nAlternatively this git repository can be cloned or the source code\ninstalled from a release archive, and then the gem created and installed\nusing:\n```rake install```\n\n## Usage\n\nTo use the library in your Ruby scripts, just require it as follows:\n```require \"rgfa\"```\n\nAdditional functionality, which\nrequires custom tags and additional conventions, is included in a separate\npart of the code named {RGFATools} and can be accessed with:\n```require \"rgfatools\"```\n\n## Documentation\n\nA cheatsheet is available as pdf under\nhttps://github.com/ggonnella/rgfa/blob/master/cheatsheet/rgfa-cheatsheet-1.3.1.pdf\n\nThe full API documentation is available as pdf under\nhttps://github.com/ggonnella/rgfa/blob/master/pdfdoc/rgfa-api-1.3.1.pdf\nor in HTML format (http://www.rubydoc.info/github/ggonnella/rgfa/master/RGFA).\n\nThe main class of the library is {RGFA}, which is a good starting point\nwhen reading the documentation.\n\n## References\n\nGonnella G, Kurtz S. (2016) RGFA: powerful and convenient handling of assembly graphs. PeerJ 4:e2681 https://doi.org/10.7717/peerj.2681 \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fggonnella%2Frgfa","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fggonnella%2Frgfa","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fggonnella%2Frgfa/lists"}