{"id":37080060,"url":"https://github.com/xie186/dragmap-meth","last_synced_at":"2026-01-14T09:42:54.398Z","repository":{"id":57423931,"uuid":"439381606","full_name":"xie186/dragmap-meth","owner":"xie186","description":"dragmap-meth: Fast and accurate aligner for bisulfite sequencing reads using dragmap","archived":true,"fork":false,"pushed_at":"2022-01-13T22:27:05.000Z","size":14347,"stargazers_count":3,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-07-11T18:46:45.688Z","etag":null,"topics":["bs-seq","dragmap"],"latest_commit_sha":null,"homepage":"https://github.com/xie186/dragmap-meth","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/xie186.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}},"created_at":"2021-12-17T15:43:35.000Z","updated_at":"2025-03-15T01:45:25.000Z","dependencies_parsed_at":"2022-09-07T04:52:31.840Z","dependency_job_id":null,"html_url":"https://github.com/xie186/dragmap-meth","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/xie186/dragmap-meth","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xie186%2Fdragmap-meth","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xie186%2Fdragmap-meth/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xie186%2Fdragmap-meth/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xie186%2Fdragmap-meth/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/xie186","download_url":"https://codeload.github.com/xie186/dragmap-meth/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xie186%2Fdragmap-meth/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28416120,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-14T08:38:59.149Z","status":"ssl_error","status_checked_at":"2026-01-14T08:38:43.588Z","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":["bs-seq","dragmap"],"created_at":"2026-01-14T09:42:53.758Z","updated_at":"2026-01-14T09:42:54.391Z","avatar_url":"https://github.com/xie186.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# dragmap_meth (dragmap_meth.py)\n\nAlignment of BS-Seq reads using [dragmap](https://github.com/Illumina/DRAGMAP). \n\n## Intro\n\nThis works for single-end reads and for **paired-end reads from the\ndirectional protocol** (most common).\n\n## Installation\n\n### Install `dragmap-meth` via `pip`\n\n`dragmap-meth` is available on https://pypi.org/project/dragmap-meth/\n\n```\npip install dragmap-meth\n```\n\n## Install `dragmap-meth` via `conda`\n\n```\nconda env create -n env4dragmap-meth --file environment.yaml python=3\ngit clone https://github.com/xie186/dragmap-meth.git\ncd dragmap-meth/\n```\n\n## QuickStart\n\nThe commands:\n\n```\npython dragmap-meth.py buildhashtable -r ref.fa -o ref/\npython  dragmap-meth.py dragmap -ht ref/ -r1 t_R1.fastq.gz -r2 t_R2.fastq.gz |samtools view -bS - -o dragmap-meth.bam\n```\n\nwill create `dragmap-meth.bam`. \nTo align single end-reads, specify only 1 file: `-r1 some_read.fastq.gz`\n\n### Dependencies\n\n```\nPython 3.10.1\ndragmap\n```\n\n## Reference:\n\nIntroducing DRAGMAP, the new genome mapper in DRAGEN-GATK: https://gatk.broadinstitute.org/hc/en-us/articles/4410953761563-Introducing-DRAGMAP-the-new-genome-mapper-in-DRAGEN-GATK\n\nDemystifying the versions of GRCh38/hg38 Reference Genomes, how they are used in DRAGEN™ and their impact on accuracy: https://www.illumina.com/science/genomics-research/articles/dragen-demystifying-reference-genomes.html\n\nhttps://github.com/DavidStreid/bio_docker/tree/main/dragmap\n\nhttps://github.com/HudsonAlpha/CSL_public_benchmark\n\n## Acknowledgement\n\nSpecial thanks to [bwa-meth](https://github.com/brentp/bwa-meth). 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