scikit-allel - Explore and analyse genetic variation

This package provides utilities for working with large scale genetic variation data using numpy, scipy and other established Python scientific libraries.

This package is in an early stage of development, if you have any questions please email Alistair Miles <>.


This package requires numpy, scipy, matplotlib, pandas, scikit-learn, h5py, numexpr, bcolz and petl. 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.

Indices and tables