{"id":15629824,"url":"https://github.com/marianattestad/ribbon","last_synced_at":"2025-05-16T15:03:25.067Z","repository":{"id":10651262,"uuid":"62266815","full_name":"MariaNattestad/Ribbon","owner":"MariaNattestad","description":"A genome browser designed for complex structural variants and long reads.","archived":false,"fork":false,"pushed_at":"2025-02-26T18:33:36.000Z","size":34962,"stargazers_count":280,"open_issues_count":15,"forks_count":30,"subscribers_count":14,"default_branch":"main","last_synced_at":"2025-04-12T12:54:41.375Z","etag":null,"topics":["bioinformatics","genome","genomics","visualization"],"latest_commit_sha":null,"homepage":"https://genomeribbon.com","language":"JavaScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MariaNattestad.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":"2016-06-30T00:31:33.000Z","updated_at":"2025-02-28T20:47:18.000Z","dependencies_parsed_at":"2022-08-26T03:00:58.624Z","dependency_job_id":"6f51473c-2565-4e82-8109-4f46bc0c9a01","html_url":"https://github.com/MariaNattestad/Ribbon","commit_stats":null,"previous_names":[],"tags_count":6,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MariaNattestad%2FRibbon","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MariaNattestad%2FRibbon/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MariaNattestad%2FRibbon/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MariaNattestad%2FRibbon/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MariaNattestad","download_url":"https://codeload.github.com/MariaNattestad/Ribbon/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254553936,"owners_count":22090415,"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","genomics","visualization"],"created_at":"2024-10-03T10:29:05.127Z","updated_at":"2025-05-16T15:03:20.826Z","avatar_url":"https://github.com/MariaNattestad.png","language":"JavaScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Ribbon/SplitThreader\n\nRibbon and SplitThreader are both visualization tools for exploring complex rearrangements and long-range structural variants. Especially if you have long reads, Ribbon and SplitThreader should be quite helpful for figuring out what's going on around large variants.\n\nRibbon is available online at [genomeribbon.com](https://genomeribbon.com)\n\n## Major changes in 2024\n\n[v2.0 release notes](docs/release_notes_v2.md)\n\n![SplitThreader to Ribbon jumping demo](images/jump_splitthreader_to_ribbon.gif)\n\nBoth built by Maria Nattestad originally, we decided in 2024 to put Ribbon and SplitThreader together and give them both major updates. This was prompted by a collaboration with the Genome in a Bottle (GIAB) team at NIST to support the release of their somatic (tumor) benchmark dataset for HG008. 2024 development done by Maria Nattestad and Robert Aboukhalil.\n\n## Documentation\n\n* How to read the visualizations? Check out [interpretation](docs/interpretation.md) for examples.\n* What changed in 2024? Including how to make a session with multiple files: [v2.0 release notes](docs/release_notes_v2.md)\n\n## Citation and publications\n\nPlease cite our paper in [_Bioinformatics_](https://doi.org/10.1093/bioinformatics/btaa680).\n\nThe BioRxiv has both the [Ribbon preprint](https://www.biorxiv.org/content/10.1101/082123v1) and the [SplitThreader preprint](https://www.biorxiv.org/content/10.1101/087981v1.full).\n\n### Ribbon\n\n![Ribbon overview](images/ribbon_overview.png)\n\n### SplitThreader\n\n![SplitThreader overview](images/splitthreader_overview.png)\n\nThere are several algorithms available within SplitThreader that can help make sense of long-range rearrangements, from categorizing variants:\n![](images/splitthreader_variant_categories_diagram.jpg)\nto searching for gene fusions:\n[gene fusion algorithms described in supplement to SplitThreader preprint](https://www.biorxiv.org/content/biorxiv/suppl/2016/11/15/087981.DC1/087981-1.pdf).\n\n## Local deployment\n\nIf you need to run Ribbon/SplitThreader without internet access, go to releases and find the ribbon_splitthreader.zip bundle from the latest release.\n\n```bash\nunzip ribbon_splitthreader.zip\ncd ribbon_splitthreader\npython3 -m http.server\n# or run any other server pointed at that directory.\n```\n\nNote that permalinks won't work without internet access.\n\n## Development and building from source\n\nTo develop new features in Ribbon, first install [npm](https://www.npmjs.com/get-npm).\n\nThen clone this repository and build it:\n\n```bash\n# Clone repo and install dependencies\ngit clone https://github.com/marianattestad/ribbon\ncd ribbon\nnpm install\n# to run locally for development\nnpm run dev\n\n# to build from source:\nnpm run build\nnpm run serve # to test the build\n# To run a server with this build:\ncd dist\npython3 -m http.server\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarianattestad%2Fribbon","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmarianattestad%2Fribbon","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarianattestad%2Fribbon/lists"}