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chanjo 2.0.0-beta

coverage analysis tool for clinical sequencing

Latest Version: 3.0.0b2

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# Chanjo [![PyPI version][fury-image]][fury-url] [![Build Status][travis-image]][travis-url] [![Coverage Status][coveralls-image]][coveralls-url]

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

## Installation
Chanjo is distruibuted through "pip". Install the latest release by running:

$ pip install chanjo

... or locally for development:

$ git clone && cd chanjo
$ pip install --editable .

Do note that Chanjo is built on some of kind-of tricky dependencies. If you are experiencing any issues, help is just a click away in the [documentation][docs].

## Usage
Chanjo exposes a composable command line interface. You can always save intermediary files at any stage and customize every option. However, using a ``chanjo.toml`` config and UNIX pipes you can end up with something like:

$ chanjo convert CCDS.sorted.txt | chanjo annotate alignment.bam > coverage.bed

## Documentation
Read the Docs is hosting the [official documentation][docs].

I can specifically recommend the fully [interactive demo]( complete with sample data to get you started right away.

## Features

### What Chanjo does
Chanjo works on BAM alignment files and extracts interesting coverage related statistics. You use a BED-file to define which regions of the genome that you particularly care about. The output takes the shape of an extended BED-file.

An optional final step is to load data into a SQL database. This will aggregate data from exons to transcripts and genes. The database will later work 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][bedtools] already handles with confidence.

## Contributors
Robin Andeer

Luca Beltrame ([lbeltrame](

## License
MIT. See the [LICENSE](LICENSE) file for more details.

## Contributing
Anyone can help make this project better - read [CONTRIBUTION]( to get started!




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chanjo-2.0.0-beta.tar.gz (md5) Source 2014-08-20 58KB
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