Chanjo

Chanjo is coverage analysis for clinical sequencing. It's implemented in Python with a command line interface that adheres to UNIX pipeline philosophy.

If you find chanjo useful in your project, please cite the article.

Installation

Chanjo is distributed through pip. Install the latest stable release by running:

pip install chanjo

... or locally for development:

git clone https://github.com/Clinical-Genomics/chanjo.git
cd chanjo
conda install --channel bioconda sambamba
pip install -r requirements-dev.txt --editable .

Usage

Chanjo exposes a decomposable command line interface with a nifty config file implementation.

chanjo init --setup
chanjo load /path/to/sambamba.output.bed
chanjo calculate mean
{"metrics": {"completeness_10": 90.92, "mean_coverage": 193.85}, "sample_id": "sample1"}

Documentation

Read the Docs is hosting the official documentation.

If you are looking to learn more about handling sequence coverage data in clinical sequencing, feel free to download and skim through my own Master's thesis and article references.

Features

What Chanjo does

Chanjo leverages Sambamba to annotate coverage and completeness for a general BED-file. The output can then easily to loaded into a SQL database that enables investigation of coverage across regions and samples. The database also works as an API to downstream tools like the Chanjo Coverage Report generator.

What Chanjo doesn't

Chanjo is not the right choice if you care about coverage for every base across the entire genome. Detailed histograms is something BEDTools already handles with confidence.

Contributors

• Robin Andeer (robinandeer)
• Luca Beltrame (lbeltrame)
• John Kern (kern3020)
• Måns Magnusson (moonso)
• Patrik Grenfeldt (patrikgrenfeldt)

License

MIT. See the LICENSE file for more details.

Contributing

Anyone can help make this project better - read CONTRIBUTION to get started!