{"id":47839988,"url":"https://github.com/barricklab/madcap-seq","last_synced_at":"2026-04-03T20:36:53.103Z","repository":{"id":92283015,"uuid":"273702422","full_name":"barricklab/mAdCap-Seq","owner":"barricklab","description":"Scripts to analyze multiplex adaptome sequencing data","archived":false,"fork":false,"pushed_at":"2021-07-12T15:21:14.000Z","size":3287,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-09-09T13:54:11.387Z","etag":null,"topics":["bioinformatics","evolution","genomics"],"latest_commit_sha":null,"homepage":"","language":"R","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/barricklab.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":"2020-06-20T12:19:32.000Z","updated_at":"2021-07-12T15:17:37.000Z","dependencies_parsed_at":"2023-06-08T06:45:39.412Z","dependency_job_id":null,"html_url":"https://github.com/barricklab/mAdCap-Seq","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/barricklab/mAdCap-Seq","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/barricklab%2FmAdCap-Seq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/barricklab%2FmAdCap-Seq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/barricklab%2FmAdCap-Seq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/barricklab%2FmAdCap-Seq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/barricklab","download_url":"https://codeload.github.com/barricklab/mAdCap-Seq/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/barricklab%2FmAdCap-Seq/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31375772,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-03T17:53:18.093Z","status":"ssl_error","status_checked_at":"2026-04-03T17:53:17.617Z","response_time":107,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 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":["bioinformatics","evolution","genomics"],"created_at":"2026-04-03T20:36:52.306Z","updated_at":"2026-04-03T20:36:53.069Z","avatar_url":"https://github.com/barricklab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Multiplex Adaptome Capture Sequencing (mAdCap-Seq)\n\nScripts and data files for the analysis pipeline described in **\"High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture sequencing\"**.\n\n## Overview\n\n* `reference` contains sequence files for the targeted genes of interest and the _E. coli_ REL606 genome with these regions masked out.\n* `consensus_read_generation` has the script for using unique molecular identifiers to perform error correction on raw Illumina reads. \n* `breseq_postprocessing` has the script for converting raw output generated by running [_breseq_](https://github.com/barricklab/breseq) on these files into a format with the read counts supporting the reference versus variant alleles. \n* `trajectory_analysis` contains the main scripts for filtering and analyzing the trajectories of mutation frequencies. \n* `LTEE-compare` and `protein_structure` contain scripts and information for further analyzing the sets of predicted mutations.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbarricklab%2Fmadcap-seq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbarricklab%2Fmadcap-seq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbarricklab%2Fmadcap-seq/lists"}