{"id":13637845,"url":"https://github.com/Illumina/manta","last_synced_at":"2025-04-19T17:32:18.798Z","repository":{"id":37752420,"uuid":"10390195","full_name":"Illumina/manta","owner":"Illumina","description":"Structural variant and indel caller for mapped sequencing data","archived":true,"fork":false,"pushed_at":"2022-12-21T13:34:23.000Z","size":118423,"stargazers_count":409,"open_issues_count":132,"forks_count":154,"subscribers_count":40,"default_branch":"master","last_synced_at":"2024-11-08T11:38:58.819Z","etag":null,"topics":["bioinformatics","indels","structural-variation","structural-variations"],"latest_commit_sha":null,"homepage":"","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/Illumina.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2013-05-30T19:33:47.000Z","updated_at":"2024-11-06T14:08:09.000Z","dependencies_parsed_at":"2023-01-30T03:46:13.103Z","dependency_job_id":null,"html_url":"https://github.com/Illumina/manta","commit_stats":null,"previous_names":[],"tags_count":75,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Illumina%2Fmanta","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Illumina%2Fmanta/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Illumina%2Fmanta/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Illumina%2Fmanta/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Illumina","download_url":"https://codeload.github.com/Illumina/manta/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":223804970,"owners_count":17205832,"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","indels","structural-variation","structural-variations"],"created_at":"2024-08-02T01:00:35.307Z","updated_at":"2024-11-09T08:30:24.433Z","avatar_url":"https://github.com/Illumina.png","language":"C++","funding_links":[],"categories":["Runtime","Next Generation Sequencing","Genomics"],"sub_categories":["Variant Calling","Mutations"],"readme":"Manta Structural Variant Caller\n===============================\n\nManta calls structural variants (SVs) and indels from mapped\npaired-end sequencing reads. It is optimized for analysis of germline\nvariation in small sets of individuals and somatic variation in\ntumor/normal sample pairs. Manta discovers, assembles and scores\nlarge-scale SVs, medium-sized indels and large insertions within a\nsingle efficient workflow. The method is designed for rapid analysis\non standard compute hardware: NA12878 at 50x genomic coverage is\nanalyzed in less than 20 minutes on a 20 core server, and most WGS\ntumor/normal analyses can be completed within 2 hours. Manta combines\npaired and split-read evidence during SV discovery and scoring to\nimprove accuracy, but does not require split-reads or successful\nbreakpoint assemblies to report a variant in cases where there is\nstrong evidence otherwise. It provides scoring models for germline\nvariants in small sets of diploid samples and somatic variants in\nmatched tumor/normal sample pairs. There is experimental support for\nanalysis of unmatched tumor samples as well. Manta accepts input read\nmappings from BAM or CRAM files and reports all SV and indel inferences\nin VCF 4.1 format. See the [user guide][UserGuide] for a full\ndescription of capabilities and limitations.\n\n[UserGuide]:docs/userGuide/README.md\n\nMethods and benchmarking details are described in:\n\nChen, X. *et al.* (2016) Manta: rapid detection of structural variants and\nindels for germline and cancer sequencing applications. *Bioinformatics*,\n32, 1220-1222. [doi:10.1093/bioinformatics/btv710][bpaper]\n\n...and the corresponding [open-access pre-print][preprint].\n\n[bpaper]:https://doi.org/10.1093/bioinformatics/btv710\n[preprint]:https://doi.org/10.1101/024232\n\n\nLicense\n-------\n\nManta source code is provided under the [GPLv3 license](LICENSE.txt).\nManta includes several third party packages provided under other\nopen source licenses, please see [COPYRIGHT.txt](COPYRIGHT.txt)\nfor additional details.\n\n\nGetting Started\n---------------\n\nFor linux users, it is recommended to start from the most recent\n[binary distribution on the Manta releases page][releases], this\ndistribution can be unpacked, moved to any convenient directory and\ntested by [running a small demo](docs/userGuide/installation.md#demo)\nincluded with the release distribution. Manta can also be installed\nand run on OS X. Please see the [installation instructions](docs/userGuide/installation.md)\nfor full build and installation details of all supported cases.\n\n[releases]:https://github.com/Illumina/manta/releases\n\n\nData Analysis and Interpretation\n--------------------------------\n\nAfter completing installation, see the [Manta user guide][UserGuide]\nfor instructions on how to run Manta, interpret results and estimate\nhardware requirements/compute cost, in addition to a high-level methods\noverview.\n\n\nManta Code Development\n----------------------\n\nFor manta code development and debugging details, see the\n[Manta developer guide][DeveloperGuide]. This includes details\non Manta's developement protocols, special build instructions,\nrecommended workflows for investigating\ncalls, and internal documentation details.\n\n[DeveloperGuide]:docs/developerGuide/README.md\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FIllumina%2Fmanta","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FIllumina%2Fmanta","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FIllumina%2Fmanta/lists"}