{"id":16637482,"url":"https://github.com/fritzsedlazeck/survivor","last_synced_at":"2025-04-05T12:08:51.946Z","repository":{"id":37743256,"uuid":"45048315","full_name":"fritzsedlazeck/SURVIVOR","owner":"fritzsedlazeck","description":"Toolset for SV simulation, comparison and filtering","archived":false,"fork":false,"pushed_at":"2023-12-01T20:05:59.000Z","size":21098,"stargazers_count":376,"open_issues_count":85,"forks_count":48,"subscribers_count":12,"default_branch":"master","last_synced_at":"2025-03-29T11:11:18.204Z","etag":null,"topics":["bioconda","bioinformatics","comparison","simulator","structural-variations","survivor","vcf"],"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/fritzsedlazeck.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}},"created_at":"2015-10-27T14:55:45.000Z","updated_at":"2025-03-28T11:55:54.000Z","dependencies_parsed_at":"2023-11-30T15:49:23.233Z","dependency_job_id":null,"html_url":"https://github.com/fritzsedlazeck/SURVIVOR","commit_stats":null,"previous_names":[],"tags_count":8,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fritzsedlazeck%2FSURVIVOR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fritzsedlazeck%2FSURVIVOR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fritzsedlazeck%2FSURVIVOR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fritzsedlazeck%2FSURVIVOR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/fritzsedlazeck","download_url":"https://codeload.github.com/fritzsedlazeck/SURVIVOR/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247332612,"owners_count":20921853,"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":["bioconda","bioinformatics","comparison","simulator","structural-variations","survivor","vcf"],"created_at":"2024-10-12T06:25:48.741Z","updated_at":"2025-04-05T12:08:51.924Z","avatar_url":"https://github.com/fritzsedlazeck.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# SURVIVOR\nSURVIVOR is a tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs.\n\n**Please see our github wiki for more information** (https://github.com/fritzsedlazeck/SURVIVOR/wiki ) \n**************************************\n## Cite:\n\nIf you use it in your study please cite:\n\n**Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast.**   \nJeffares, Daniel C; Jolly, Clemency; Hoti, Mimoza; Speed, Doug; Shaw, Liam; Rallis, Charalampos; Balloux, Francois; Dessimoz, Christophe; Bähler, Jürg; Sedlazeck, Fritz J.   \nNature communications, Vol. 8, 14061, 24.01.2017, p. 1-11. DOI:10.1038/NCOMMS14061\n\n**************************************\n\n## INSTALL:\n\nDownload SURVIVOR:\n\u003cpre\u003e\ngit clone https://github.com/fritzsedlazeck/SURVIVOR.git\ncd SURVIVOR/Debug\nmake\n\u003c/pre\u003e\n\n**************************************\n\n## USAGE:\n```\n./SURVIVOR ID\n```\nto see the individual parameters for each option.\n\nchoose the ID from these options:\n```\nProgram: SURVIVOR (Tools for Structural Variations in the VCF format)\nVersion: 1.0.3\n\nUsage: SURVIVOR \u003ccommand\u003e [options]\n\nCommands:\n-- Simulation/ Evaluation\n\tsimSV\tSimulates SVs and SNPs on a reference genome.\n\tscanreads\tObtain error profiles form mapped reads for simulation.\n\tsimreads\tSimulates long reads (Pacio or ONT).\n\teval\tEvaluates a VCF file after SV calling over simulated data.\n\n-- Comparison/filtering\n\tmerge\tCompare or merge VCF files to generate a consensus or multi sample vcf files.\n\tfilter\tFilter a vcf file based on size and/or regions to ignore\n\tstats\tReport multipe stats over a VCF file\n\tcompMUMMer\tAnnotates a VCF file with the breakpoints found with MUMMer (Show-diff).\n\n-- Conversion\n\tbincov\tBins coverage vector to a bed file to filter SVs in low MQ regions\n\tvcftobed\tConverts a VCF file to a bed file\n\tbedtovcf\tConverts a bed file to a VCF file\n\tsmaptovcf\tConverts the smap file to a VCF file (beta version)\n\tbedpetovcf\tConverts a bedpe file ot a VCF file (beta version)\n\thapcuttovcf\tConverts the Hapcut2 final file to a VCF file using the original SNP file provided to Hapcut2\n\tconvertAssemblytics\tConverts Assemblytics to a VCF file```\n```\n**************************************\n## CONTACT:\n\nIf you have questions or encounter a problem please contact:\nfritz.sedlazeck@gmail.com\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffritzsedlazeck%2Fsurvivor","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffritzsedlazeck%2Fsurvivor","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffritzsedlazeck%2Fsurvivor/lists"}