{"id":49883360,"url":"https://github.com/mikessh/mageri","last_synced_at":"2026-05-15T16:11:46.465Z","repository":{"id":71694851,"uuid":"26858760","full_name":"mikessh/mageri","owner":"mikessh","description":"MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers","archived":false,"fork":false,"pushed_at":"2017-05-08T22:17:54.000Z","size":104589,"stargazers_count":21,"open_issues_count":9,"forks_count":6,"subscribers_count":5,"default_branch":"master","last_synced_at":"2026-01-15T08:17:35.602Z","etag":null,"topics":["amplicon","bioinformatics","cancer","ctdna","exon","mapping","mutation","umi","variant"],"latest_commit_sha":null,"homepage":"http://mageri.readthedocs.org/en/latest/","language":"Java","has_issues":false,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mikessh.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":"2014-11-19T11:40:59.000Z","updated_at":"2024-06-07T14:55:36.000Z","dependencies_parsed_at":null,"dependency_job_id":"48d9e68a-d4b8-4508-9154-981402eb93e9","html_url":"https://github.com/mikessh/mageri","commit_stats":null,"previous_names":["mikessh/oncomigec"],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/mikessh/mageri","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mikessh%2Fmageri","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mikessh%2Fmageri/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mikessh%2Fmageri/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mikessh%2Fmageri/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mikessh","download_url":"https://codeload.github.com/mikessh/mageri/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mikessh%2Fmageri/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33071699,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-15T11:35:32.926Z","status":"ssl_error","status_checked_at":"2026-05-15T11:35:31.362Z","response_time":103,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 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":["amplicon","bioinformatics","cancer","ctdna","exon","mapping","mutation","umi","variant"],"created_at":"2026-05-15T16:11:45.717Z","updated_at":"2026-05-15T16:11:46.454Z","avatar_url":"https://github.com/mikessh.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"MAGERI\n======\n\n[![Build Status](https://travis-ci.org/mikessh/mageri.svg?branch=master)](https://travis-ci.org/mikessh/mageri)\n\n[Molecular tagging approach](http://www.pnas.org/content/108/23/9530) has revolutionized the field of high depth genome re-sequencing \nby allowing detection of ultra-rare mutations. This pipeline aims at filling the gap in software for analysis of UMI-tagged data. \nMAGERI implements consensus assembly, alignment and variant calling and allows to process \ndatasets into ready SAM and VCF files in a single command. Its main purpose is to analyze targeted region genome re-sequencing data for tumor heterogeneity and circulating tumor DNA studies, however it can be also applied to other tasks that require accurate rare variant detection.\n\nSee [mageri-paper repository](https://github.com/mikessh/mageri-paper) for examples and supplementary data.\n\nSoftware binaries can be found in the [releases section](https://github.com/mikessh/mageri/releases/latest), the documentation is available [here](http://mageri.readthedocs.io/en/latest/).\n\nPlease cite the software as [Shugay et al. Plos Comp Biol 2017](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005480).","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmikessh%2Fmageri","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmikessh%2Fmageri","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmikessh%2Fmageri/lists"}