scikit-allel - Explore and analyse genetic variation

This package provides utilities for exploratory analysis of large scale genetic variation data. It is based on numpy, scipy and other established Python scientific libraries.

If you have any questions, find a bug, or would like to suggest a feature, please raise an issue on GitHub.

This site provides reference documentation for scikit-allel. For worked examples with real data, see the following articles:

If you would like to cite scikit-allel please use the DOI below.


This package requires numpy, scipy, matplotlib, seaborn, pandas, scikit-learn, h5py, numexpr, bcolz and petl. Please install these dependencies first, then use pip to install scikit-allel:

$ pip install -U scikit-allel


Development of this package is supported by the MRC Centre for Genomics and Global Health.

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