{"id":23071264,"url":"https://github.com/clinical-genomics/chanjo","last_synced_at":"2026-05-08T09:02:32.491Z","repository":{"id":9349168,"uuid":"11200045","full_name":"Clinical-Genomics/chanjo","owner":"Clinical-Genomics","description":"Chanjo provides a better way to analyze coverage data in clinical sequencing.","archived":false,"fork":false,"pushed_at":"2026-05-08T08:06:28.000Z","size":15436,"stargazers_count":50,"open_issues_count":33,"forks_count":12,"subscribers_count":8,"default_branch":"main","last_synced_at":"2026-05-08T08:18:19.552Z","etag":null,"topics":["bioconda","coverage","genomics","python","sambamba","sql"],"latest_commit_sha":null,"homepage":"https://clinical-genomics.github.io/chanjo/","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/Clinical-Genomics.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"CONTRIBUTING.md","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":"AUTHORS","dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2013-07-05T13:22:17.000Z","updated_at":"2026-05-08T08:05:21.000Z","dependencies_parsed_at":"2023-01-13T15:18:33.866Z","dependency_job_id":"8fa72aec-7570-4665-adf1-3d6b2a27ad2c","html_url":"https://github.com/Clinical-Genomics/chanjo","commit_stats":null,"previous_names":["robinandeer/chanjo"],"tags_count":52,"template":false,"template_full_name":null,"purl":"pkg:github/Clinical-Genomics/chanjo","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Clinical-Genomics%2Fchanjo","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Clinical-Genomics%2Fchanjo/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Clinical-Genomics%2Fchanjo/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Clinical-Genomics%2Fchanjo/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Clinical-Genomics","download_url":"https://codeload.github.com/Clinical-Genomics/chanjo/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Clinical-Genomics%2Fchanjo/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32773858,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-08T08:22:46.396Z","status":"ssl_error","status_checked_at":"2026-05-08T08:22:45.650Z","response_time":54,"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":["bioconda","coverage","genomics","python","sambamba","sql"],"created_at":"2024-12-16T07:12:55.841Z","updated_at":"2026-05-08T09:02:32.422Z","avatar_url":"https://github.com/Clinical-Genomics.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://github.com/Clinical-Genomics/chanjo\"\u003e\n    \u003cimg height=\"235\" width=\"244\" src=\"docs/assets/logo.png\"/\u003e\n  \u003c/a\u003e\n\u003c/p\u003e\n\n# Chanjo \n![Docker build - GitHub](https://github.com/Clinical-Genomics/chanjo/actions/workflows/docker_build_n_publish.yml/badge.svg)\n[![PyPI version](https://badge.fury.io/py/chanjo.svg)](https://badge.fury.io/py/chanjo)\n[![Coverage Status](https://coveralls.io/repos/github/Clinical-Genomics/chanjo/badge.svg?branch=master)](https://coveralls.io/github/Clinical-Genomics/chanjo?branch=master)\n\n\nChanjo is coverage analysis for clinical sequencing. It's implemented in Python\nwith a command line interface that adheres to [UNIX pipeline philosophy][unix].\n\nIf you find chanjo useful in your project, please cite the [article][publication].\n\n## Installation\nChanjo is distributed through `pip`. Install the latest stable release by\nrunning:\n\n```bash\npip install chanjo\n```\n\n... or locally for development:\n\n```bash\ngit clone https://github.com/Clinical-Genomics/chanjo.git\ncd chanjo\nconda install --channel bioconda sambamba\npip install -r requirements-dev.txt --editable .\n```\n\n## Usage\nChanjo exposes a decomposable command line interface with a nifty config file\nimplementation.\n\n```bash\nchanjo init --setup\nchanjo load /path/to/sambamba.output.bed\nchanjo calculate mean\n{\"metrics\": {\"completeness_10\": 90.92, \"mean_coverage\": 193.85}, \"sample_id\": \"sample1\"}\n```\n\n## Docker\n\nWhen running the dockerized version of [Chanjo](https://hub.docker.com/r/clinicalgenomics/chanjo) the setup process is slightly different. Chanjo depends on a configuration file `config.yaml` and either a sqlite database `chanjo.coverage.sqlite3` or a `MySQL database`, which are created at initialization. For convenience, we provide a docker-compose file containing a mariadb (MySQL-based) service and the chanjo-command line that can be used to set up a demo instance of Chanjo.\nSince the database set up (chanjo init command) and sample data insertion are executed by two distinct instances of the same service (chanjo-cli), Docker [volumes](https://docs.docker.com/storage/volumes/) must be used to make sure that the database instance has data continuity during the two steps.\nThe following examples demonstrate how to set up Chanjo using the docker-compose file using the default definition of exons (init demo files are present in folder `chanjo/init/demo-files`). The config file and the creted database will be stored on the host in a folder named `data`, which is mirrored by folder `/home/worker/data` in the chanjo container . Other exon definitions can be used by mounting them to the container.\n\n### Example with MySQL-based database (MariaDB)\n\n```bash\n# Build a docker image\ndocker-compose build\n```\n```bash\n# Set up chanjo and populate demo database with exons definitions\ndocker-compose run --rm -v \"${PWD}/data:/home/worker/data\" -v \"${PWD}/data/database:/home/worker/data/database\" chanjo-cli bash -c \"chanjo -d mysql+pymysql://chanjoUser:chanjoPassword@mariadb/chanjo4_test init --auto /home/worker/data \u0026\u0026 chanjo --config /home/worker/data/chanjo.yaml link /home/worker/data/hgnc.grch37p13.exons.bed\"\n```\nThis initial step will create a `data` folder containing 2 files:\n- hgnc.grch37p13.exons.bed --\u003e Exons definitions\n- chanjo.yaml --\u003e Contains the database URI, so in the next step you can use this config file instead of `-d mysql+pymysql://chanjoUser:chanjoPassword@mariadb/chanjo4_test`\n\n```bash\n# Load sample\ndocker-compose run --rm -v \"${PWD}/data:/home/worker/data\" -v \"${PWD}/data/database:/home/worker/data/database\" chanjo-cli bash -c \"chanjo --config /home/worker/data/chanjo.yaml load /home/worker/app/chanjo/init/demo-files/sample1.coverage.bed\"\n```\n\n### Example with SQLite database\n\n```bash\n# setup chanjo and save populate demo database with exon definitions\ndocker-compose run --rm -v \"${PWD}/data:/home/worker/data\" -v \"${PWD}/data/database:/home/worker/data/database\" chanjo-cli bash -c \"chanjo init --auto /home/worker/data \u0026\u0026 chanjo --config /home/worker/data/chanjo.yaml link /home/worker/data/hgnc.grch37p13.exons.bed\"\n# load sample\ndocker-compose run --rm -v \"${PWD}/data/chanjo.coverage.sqlite3:/home/worker/app/chanjo.coverage.sqlite3\" -v \"${PWD}/data:/home/worker/data\" chanjo-cli bash -c \"chanjo --config /home/worker/data/chanjo.yaml load /home/worker/app/chanjo/init/demo-files/sample1.coverage.bed\"\n\n## Documentation\nRead the Docs is hosting the [official documentation][docs].\n\nIf you are looking to learn more about handling sequence coverage data in\nclinical sequencing, feel free to download and skim through my own\n[Master's thesis][thesis] and article references.\n\n## Features\n\n### What Chanjo does\nChanjo leverages [Sambamba][sambamba] to annotate coverage and completeness\nfor a general BED-file. The output can then easily to loaded into a SQL\ndatabase that enables investigation of coverage across regions and samples.\nThe database also works as an API to downstream tools like the Chanjo\nCoverage Report generator.\n\n### What Chanjo doesn't\nChanjo is not the right choice if you care about coverage for every base across\nthe entire genome. Detailed histograms is something [BEDTools][bedtools]\nalready handles with confidence.\n\n## Contributors\n-   Robin Andeer ([robinandeer](https://github.com/robinandeer))\n-   Luca Beltrame ([lbeltrame](https://github.com/lbeltrame))\n-   John Kern ([kern3020](https://github.com/kern3020))\n-   Måns Magnusson ([moonso](https://github.com/moonso))\n-   Patrik Grenfeldt ([patrikgrenfeldt](https://github.com/patrikgrenfeldt))\n\n## License\nMIT. See the [LICENSE](LICENSE) file for more details.\n\n## Contributing\nAnyone can help make this project better - read [CONTRIBUTION](CONTRIBUTION.md)\nto get started!\n\n[bedtools]: http://bedtools.readthedocs.org/en/latest/\n[docs]: https://clinical-genomics.github.io/chanjo/\n[publication]: https://f1000research.com/articles/9-615/v1\n[sambamba]: http://lomereiter.github.io/sambamba/\n[thesis]: https://s3.amazonaws.com/tudo/chanjo/RobinAndeerMastersThesisFinal_2013.pdf\n[unix]: http://en.wikipedia.org/wiki/Unix_philosophy\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fclinical-genomics%2Fchanjo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fclinical-genomics%2Fchanjo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fclinical-genomics%2Fchanjo/lists"}