Hail is an open-source, scalable framework for exploring and analyzing genomic data.

The Hail project began in Fall 2015 to empower the worldwide genetics community to harness the flood of genomes to discover the biology of human disease. Since then, Hail has expanded to enable analysis of large-scale datasets beyond the field of genomics.

We’re running an introductory Hail workshop in Boston on October 31, hosted by the Harvard School of Public Health. Reserve a spot here.

Here are two examples of projects powered by Hail:

For genomics applications, Hail can:

Hail’s functionality is exposed through Python and backed by distributed algorithms built on top of Apache Spark to efficiently analyze gigabyte-scale data on a laptop or terabyte-scale data on a cluster.

Users can script pipelines or explore data interactively in Jupyter notebooks that combine Hail’s methods, PySpark’s scalable SQL and machine learning algorithms, and Python libraries like pandas, scikit-learn and inline plotting.

To learn more, you can view our talks at Spark Summit East 2017 and Spark Summit West 2017.

Getting Started

To get started using Hail:

User Support

There are many ways to get in touch with the Hail team if you need help using Hail, or if you would like to suggest improvements or features. We also love to hear from new users about how they are using Hail.

Hail uses a continuous deployment approach to software development, which means we frequently add new features. We update users about changes to Hail via the Discussion Forum. We recommend creating an account on the Discussion Forum so that you can subscribe to these updates.

Contribute

Hail is committed to open-source development. Our Github repo is publicly visible. If you’d like to contribute to the development of methods or infrastructure, please:

Hail Team

The Hail team is embedded in the Neale lab at the Stanley Center for Psychiatric Research of the Broad Institute of MIT and Harvard and the Analytic and Translational Genetics Unit of Massachusetts General Hospital.

Contact the Hail team at hail@broadinstitute.org.

Follow Hail on Twitter @hailgenetics.

Citing Hail

If you use Hail for published work, please cite the software:

Acknowledgements

We would like to thank Zulip for supporting open-source by providing free hosting, and YourKit, LLC for generously providing free licenses for YourKit Java Profiler for open-source development.