{"id":24699067,"url":"https://github.com/laura-budurlean/sv-calling-with-speedseq","last_synced_at":"2025-03-22T03:43:00.311Z","repository":{"id":155521351,"uuid":"631047804","full_name":"laura-budurlean/SV-calling-with-SpeedSeq","owner":"laura-budurlean","description":"A workflow for using SpeedSeq to align and call SVs from WGS data","archived":false,"fork":false,"pushed_at":"2024-08-24T06:07:23.000Z","size":16,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-27T04:35:10.098Z","etag":null,"topics":["bioinformatics","cnv","delly","freebayes","lumpy","speedseq","structural-variation","sv"],"latest_commit_sha":null,"homepage":"https://github.com/laura-budurlean/SV-calling-with-SpeedSeq","language":"Shell","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/laura-budurlean.png","metadata":{"files":{"readme":"README.md","changelog":null,"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":"2023-04-21T19:41:18.000Z","updated_at":"2024-08-24T06:07:26.000Z","dependencies_parsed_at":null,"dependency_job_id":"ab965851-abc5-4f6d-8396-571a2ca9b09e","html_url":"https://github.com/laura-budurlean/SV-calling-with-SpeedSeq","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/laura-budurlean%2FSV-calling-with-SpeedSeq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/laura-budurlean%2FSV-calling-with-SpeedSeq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/laura-budurlean%2FSV-calling-with-SpeedSeq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/laura-budurlean%2FSV-calling-with-SpeedSeq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/laura-budurlean","download_url":"https://codeload.github.com/laura-budurlean/SV-calling-with-SpeedSeq/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244902921,"owners_count":20529114,"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","cnv","delly","freebayes","lumpy","speedseq","structural-variation","sv"],"created_at":"2025-01-27T04:35:16.354Z","updated_at":"2025-03-22T03:43:00.291Z","avatar_url":"https://github.com/laura-budurlean.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# SV-calling-with-SpeedSeq\nA workflow for using SpeedSeq to align and call SVs from WGS data. A simple guide to SpeedSeq to get SNV, SVs, and to generate normal, discordant, and splitter BAM files. SNV calling with Freebayes, SV calling with LUMPY DELLY is included.\n\nSee speedseq_pipeline file for details.\nAdditional information on SpeedSeq is available from the Hall lab at: https://github.com/hall-lab/speedseq and https://www.nature.com/articles/nmeth.3505\n\n# SpeedSeq pipeline overview:\n![speedseq](https://github.com/laura-budurlean/SV-calling-with-SpeedSeq/assets/30268603/c42cdbc2-a77c-46fb-873e-2d67a85bb485)\nImage reproduced from: https://www.nature.com/articles/nmeth.3505\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flaura-budurlean%2Fsv-calling-with-speedseq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flaura-budurlean%2Fsv-calling-with-speedseq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flaura-budurlean%2Fsv-calling-with-speedseq/lists"}