{"id":16619264,"url":"https://github.com/brwnj/covdist","last_synced_at":"2026-03-12T00:05:36.787Z","repository":{"id":149765493,"uuid":"362217601","full_name":"brwnj/covdist","owner":"brwnj","description":"simple coverage distribution profile of aligned samples. useful for sequencing center feedback and topoffs.","archived":false,"fork":false,"pushed_at":"2022-05-20T15:58:54.000Z","size":90,"stargazers_count":4,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-12-13T22:27:32.871Z","etag":null,"topics":["coverage","genomics-visualization"],"latest_commit_sha":null,"homepage":"https://brwnj.github.io/covdist/","language":"HTML","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/brwnj.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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2021-04-27T18:46:53.000Z","updated_at":"2023-02-09T19:35:09.000Z","dependencies_parsed_at":"2023-04-25T17:33:16.781Z","dependency_job_id":null,"html_url":"https://github.com/brwnj/covdist","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/brwnj/covdist","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brwnj%2Fcovdist","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brwnj%2Fcovdist/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brwnj%2Fcovdist/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brwnj%2Fcovdist/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/brwnj","download_url":"https://codeload.github.com/brwnj/covdist/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brwnj%2Fcovdist/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30407844,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-11T22:36:59.286Z","status":"ssl_error","status_checked_at":"2026-03-11T22:36:57.544Z","response_time":84,"last_error":"SSL_read: 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":["coverage","genomics-visualization"],"created_at":"2024-10-12T02:24:47.382Z","updated_at":"2026-03-12T00:05:36.782Z","avatar_url":"https://github.com/brwnj.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# covdist\nPerform simple coverage profiling of aligned samples. Admittedly this is\na very simple tool, but is quite useful for sequencing center feedback and\ntopoffs.\n\nInteractive example: https://brwnj.github.io/covdist/\n\n## Note\n\nThis is an extension of mosdepth's plot-dist.py script. See:\nhttps://github.com/brentp/mosdepth/blob/master/scripts/plot-dist.py\n\nHere we run `mosdepth` and generate a very similar report.\n\n# Usage\n\n```\nnextflow run brwnj/covdist -revision main -profile docker\n    --crams '*.cram'\n    --reference GRCh38.fasta\n    --gaps GRCh38_gaps.bed\n```\n\n## Gap info\n\nA simple way to grab this info, to omit region of known gaps in coverage, is\nto head over to:\n\nhttps://genome.ucsc.edu/cgi-bin/hgTables\n\n1. Under `group:` select `Mapping and Sequencing`.\n2. For `track:` select `Gap`\n3. Set `output format:` as `BED` and define the file name.\n\n## Autosomes\n\nIt is likely important for you to get accurate coverage estimates and to\ncommunicate them with your sequencing center. That said, you likely want\nto exclude sex chromosomes using:\n\n```\n--exclude \"decoy,random,chrUn,alt,phix,chrEBV,chrM,chrX,chrY\"\n```\n\n# Report\n\nSamples can be subset using the \"Samples\" filter, which is sorted by ascending median coverage.\n\nYou can browse covered on each chromosome or all chromosomes under the label \"total\".\n\nTarget coverage cutoff is set dynamically by the user and updates the table. The table\ncolumn is sortable and selections on the table can be made to highlight a given sample.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrwnj%2Fcovdist","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbrwnj%2Fcovdist","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrwnj%2Fcovdist/lists"}