{"id":13704001,"url":"https://github.com/luntergroup/octopus","last_synced_at":"2026-01-14T22:25:28.457Z","repository":{"id":26831858,"uuid":"30291133","full_name":"luntergroup/octopus","owner":"luntergroup","description":"Bayesian haplotype-based mutation calling","archived":false,"fork":false,"pushed_at":"2025-11-27T08:45:37.000Z","size":145275,"stargazers_count":321,"open_issues_count":60,"forks_count":36,"subscribers_count":16,"default_branch":"develop","last_synced_at":"2025-12-06T20:27:50.281Z","etag":null,"topics":["bioinformatics","de-novo-mutation","genomics","haplotypes","phasing","single-cell","somatic-variants","variant-calling","variants"],"latest_commit_sha":null,"homepage":"","language":"C++","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/luntergroup.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2015-02-04T09:24:53.000Z","updated_at":"2025-11-21T08:50:42.000Z","dependencies_parsed_at":"2022-07-21T22:00:16.260Z","dependency_job_id":"3ab3cef9-a9ba-44f5-ab37-81c7c1733429","html_url":"https://github.com/luntergroup/octopus","commit_stats":null,"previous_names":[],"tags_count":35,"template":false,"template_full_name":null,"purl":"pkg:github/luntergroup/octopus","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/luntergroup%2Foctopus","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/luntergroup%2Foctopus/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/luntergroup%2Foctopus/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/luntergroup%2Foctopus/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/luntergroup","download_url":"https://codeload.github.com/luntergroup/octopus/tar.gz/refs/heads/develop","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/luntergroup%2Foctopus/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28436313,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-14T21:32:52.117Z","status":"ssl_error","status_checked_at":"2026-01-14T21:32:33.442Z","response_time":107,"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":["bioinformatics","de-novo-mutation","genomics","haplotypes","phasing","single-cell","somatic-variants","variant-calling","variants"],"created_at":"2024-08-02T21:01:02.811Z","updated_at":"2026-01-14T22:25:28.436Z","avatar_url":"https://github.com/luntergroup.png","language":"C++","funding_links":[],"categories":["Next Generation Sequencing","Software packages"],"sub_categories":["Variant Calling","Variant calling"],"readme":"![Octopus Logo](logo.png)\n\n[![Website](https://img.shields.io/website?url=https%3A%2F%2Fluntergroup.github.io%2Foctopus%2F)](https://luntergroup.github.io/octopus/)\n[![Build Status](https://travis-ci.org/luntergroup/octopus.svg?branch=master)](https://travis-ci.org/luntergroup/octopus)\n[![MIT license](http://img.shields.io/badge/license-MIT-brightgreen.svg)](http://opensource.org/licenses/MIT)\n[![Gitter](https://badges.gitter.im/octopus-caller/Lobby.svg)](https://gitter.im/octopus-caller/Lobby?utm_source=badge\u0026utm_medium=badge\u0026utm_campaign=pr-badge)\n![GitHub release (latest SemVer)](https://img.shields.io/github/v/release/luntergroup/octopus)\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/octopus/badges/installer/conda.svg)](https://conda.anaconda.org/bioconda)\n[![Docker Image Version (latest semver)](https://img.shields.io/docker/v/dancooke/octopus?label=docker)](https://hub.docker.com/r/dancooke/octopus)\n\nOctopus is a mapping-based variant caller that implements several calling models within a unified haplotype-aware framework. Octopus takes inspiration from particle filtering by constructing a tree of haplotypes and dynamically pruning and extending the tree based on haplotype posterior probabilities in a sequential manner. This allows octopus to implicitly consider all possible haplotypes at a given loci in reasonable time.\n\nThere are currently six calling models available:\n\n- [individual](https://luntergroup.github.io/octopus/docs/guides/models/individual): call germline variants in a single healthy individual.\n- [population](https://luntergroup.github.io/octopus/docs/guides/models/population): jointly call germline variants in small cohorts.\n- [trio](https://luntergroup.github.io/octopus/docs/guides/models/trio): call germline and _de novo_ mutations in a parent-offspring trio.\n- [cancer](https://luntergroup.github.io/octopus/docs/guides/models/cancer): call germline and somatic mutations tumour samples.\n- [polyclone](https://luntergroup.github.io/octopus/docs/guides/models/polyclone): call variants in samples with an unknown mixture of haploid clones, such a bacteria or viral samples.\n- [cell](https://luntergroup.github.io/octopus/docs/guides/models/cell): call variants in a set of single cell samples from the same individual.\n\nOctopus calls SNVs, small-medium sized indels, and small complex rearrangements in [VCF 4.3](https://luntergroup.github.io/octopus/docs/guides/advanced/vcf).\n\n## Quick start\n\nInstall Octopus:\n\n```shell\n$ git clone https://github.com/luntergroup/octopus.git\n$ octopus/scripts/install.py --dependencies --forests\n$ echo 'export PATH='$(pwd)'/octopus/bin:$PATH' \u003e\u003e ~/.bash_profile\n$ source ~/.bash_profile\n```\n\nCall some variants:\n\n```shell\n$ FOREST=\"$(pwd)/octopus/resources/forests/germline.v0.7.4.forest\"\n$ octopus -R hs37d5.fa -I NA12878.bam -T 1 to MT -o NA12878.octopus.vcf.gz --forest $FOREST --threads 8\n```\n\n## Documentation\n\nDocumentation is hosted on [GitHub pages](https://luntergroup.github.io/octopus/).\n\n## Support\n\nPlease report any bugs or feature requests to the [octopus issue tracker](https://github.com/luntergroup/octopus/issues). General chat is hosted on [Gitter](https://gitter.im/octopus-caller/Lobby).\n\n## Contributing\n\nContributions are very welcome! Please consult the [contribution guidelines](CONTRIBUTING.md).\n\n## Authors\n\nDaniel Cooke and Gerton Lunter\n\n## Citing\n\nSee [publications](https://luntergroup.github.io/octopus/docs/publications) associated with Octopus.\n\n## License\n\nOctopus is distributed under the [MIT LICENSE](LICENSE).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fluntergroup%2Foctopus","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fluntergroup%2Foctopus","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fluntergroup%2Foctopus/lists"}