{"id":25501957,"url":"https://github.com/opengene/dedup","last_synced_at":"2025-07-08T20:14:09.174Z","repository":{"id":90140080,"uuid":"96286989","full_name":"OpenGene/dedup","owner":"OpenGene","description":"Deduplication for cfDNA sequencing data","archived":false,"fork":false,"pushed_at":"2017-07-05T07:13:03.000Z","size":4,"stargazers_count":11,"open_issues_count":2,"forks_count":4,"subscribers_count":10,"default_branch":"master","last_synced_at":"2025-04-10T09:54:08.121Z","etag":null,"topics":["bioinformatics","ctdna","deduplication","liquid","ngs"],"latest_commit_sha":null,"homepage":null,"language":"Python","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/OpenGene.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-07-05T06:56:30.000Z","updated_at":"2025-01-12T13:14:18.000Z","dependencies_parsed_at":null,"dependency_job_id":"6139f4df-79c3-4a5d-86ca-76a83a260b67","html_url":"https://github.com/OpenGene/dedup","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/OpenGene/dedup","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenGene%2Fdedup","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenGene%2Fdedup/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenGene%2Fdedup/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenGene%2Fdedup/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/OpenGene","download_url":"https://codeload.github.com/OpenGene/dedup/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenGene%2Fdedup/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":264341130,"owners_count":23593298,"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","ctdna","deduplication","liquid","ngs"],"created_at":"2025-02-19T04:59:48.464Z","updated_at":"2025-07-08T20:14:09.169Z","avatar_url":"https://github.com/OpenGene.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# dedup\nA small script for NGS data deduplication, optimized for cfDNA sequencing data\n\n# Dependency\nThis script depends on `pysam` module, please install it by `pip` or `easy_install` first\n\n# Usage\n```shell\n./dedup.py -1 in.sorted.bam -o out.bam \u003e dedup.log\n```\nBe sure that the in.sorted.bam is sorted\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopengene%2Fdedup","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fopengene%2Fdedup","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopengene%2Fdedup/lists"}