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Chanjo - Coverage analysis for clinical sequencing


Chanjo is mainly used as a command line utility backed by a thin Python API.

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

To learn more about Chanjo and how you can use it to gain a better understanding of sequencing coverage you should start by checking out the demo.

Whats new in Chanjo 3.0? Radical Red Panda

Chanjo 3 is a significant improvement of the previous versions.

The primary change is Sambamba integration. Just run `sambamba depth region` and load the output into Chanjo for further data exploration. Chanjo is now more flexible, accurate, and much easier to install. We have also built in some basic commands to quickly extract statistics from the database right from the command line.


Chanjo can help you extract coverage statistics from BAM alignments. It allows you to pool multiple samples and calculate aggregated metrics. The data can also be used by downstream tools like the Chanjo Report generator.


The comprehensive documentation has all the information you want; getting started guide, installation instructions, and in-depth overviews.

Installation PyPI version Build Status

Complete instructions are available in the docs but if you know what you are doing, Chanjo is installed by simply running:

$ pip install chanjo


Luca Beltrame (lbeltrame)

John Kern (kern3020)

Måns Magnusson (moonso)



See the code for Chanjo here: https://github.com/robinandeer/chanjo