{"id":20425050,"url":"https://github.com/databio/ref_decoy","last_synced_at":"2026-03-10T05:03:03.157Z","repository":{"id":86287803,"uuid":"78471398","full_name":"databio/ref_decoy","owner":"databio","description":"Decoy alignment sequences","archived":false,"fork":false,"pushed_at":"2022-01-06T21:31:34.000Z","size":219,"stargazers_count":5,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-09-11T10:15:49.444Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"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/databio.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":"2017-01-09T21:38:01.000Z","updated_at":"2024-08-02T03:44:29.000Z","dependencies_parsed_at":"2023-03-13T09:28:31.751Z","dependency_job_id":null,"html_url":"https://github.com/databio/ref_decoy","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/databio/ref_decoy","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fref_decoy","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fref_decoy/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fref_decoy/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fref_decoy/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/databio","download_url":"https://codeload.github.com/databio/ref_decoy/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fref_decoy/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30325599,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-10T01:36:58.598Z","status":"online","status_checked_at":"2026-03-10T02:00:06.579Z","response_time":106,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":[],"created_at":"2024-11-15T07:12:08.054Z","updated_at":"2026-03-10T05:03:03.140Z","avatar_url":"https://github.com/databio.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# Genome assembly decoy sequences\n\nThis repository contains fasta files for pre-alignments. These are useful for studies of repeats, mtDNA, or using as decoy sequences.\n\n## Contents:\n\n### Repeats\n\n* human_alu.fa - Manually curated sequences from GenBank for alu elements.\n* human_alphasat.fa - Manually curated sequences from GenBank annotated for centromeric or alpha-satellite DNA repeats.\n* human_rDNA.fa - Complete human ribosomal repeat unit\n* mouse_rDNA.fa - Complete mouse ribosomal repeat unit (from GenBank).\n* human_repeats.fa: a combination of the 3 of above (alu, alphasat, and rDNA) , produced with `cat human_alu.fa human_alphasat.fa human_rDNA.fa \u003e human_repeats.fa`.\n\n### mtDNA\n\n* rCRSd.fa is the Revised Cambridge Reference Sequence (rCRS) of the Human Mitochondrial DNA obtained from [NC_012920](http://www.ncbi.nlm.nih.gov/nuccore/251831106). It is duplicated (pasted 2 times, one right after another) to simulate circular DNA for aligners that do not have a circular setting (hence the appended `d` to the name). This is the assembly used in hg38.\n* RSRS.fa is from [this paper](http://dx.doi.org/10.1016/j.ajhg.2012.03.002).\n* eve1.fa is from [this paper](http://dx.doi.org/10.1093/nar/gkm207).\n* human_chrM2x - Doubled chrM derived from [AF347015](http://www.ncbi.nlm.nih.gov/nuccore/13273284), the African Yoruban sequence used in the hg19 assembly.\n* mouse_chrM2x - Doubled chrM derived from mm10 reference.\n\n## Pre-built indexes\n\nYou can download pre-built [refgenie](http://www.github.com/databio/refgenie) reference genomes indexes for use in pipelines here:\n\n* [list of pre-built indexes](http://big.databio.org/refgenomes/)\n\nTo use these with [pypiper](http://www.databio.org/pypiper) pipelines, just unzip the folder and place in your genomes folder (e.g. `$GENOMES`).\n\n## Built it yourself\n\nBuild genome references for these decoy sequences using [refgenie](http://github.com/databio/refgenie) like this:\n\n```\nrefgenie.py -i hg19_alphasat.fa\n```\n\nA complete setup:\n\n```\nGENOMES=decoy_genomes\n\npip install --user --upgrade https://github.com/epigen/pypiper/zipball/master\ngit clone https://github.com/databio/ref_decoy.git\ngit clone https://github.com/databio/refgenie.git\n\nfor fa_file in `ls ref_decoy/*.fa`; do python refgenie/src/refgenie.py -i $fa_file; done\n```\n\nOr, using the refgenie docker image (adds `-d`):\n\n```\nfor fa_file in `ls ref_decoy/*.fa`; do python refgenie/src/refgenie.py -d -i $fa_file; done\n```\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fref_decoy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatabio%2Fref_decoy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fref_decoy/lists"}