https://github.com/sgkit-dev/sgkit

Scalable genetics toolkit
https://github.com/sgkit-dev/sgkit

genetics gwas popgen pydata statgen statistical-genetics

Last synced: about 1 month ago
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Scalable genetics toolkit

• Host: GitHub
• URL: https://github.com/sgkit-dev/sgkit
• Owner: sgkit-dev
• License: apache-2.0
• Created: 2020-06-16T17:58:57.000Z (almost 6 years ago)
• Default Branch: main
• Last Pushed: 2026-03-02T15:20:11.000Z (2 months ago)
• Last Synced: 2026-03-02T18:42:25.722Z (2 months ago)
• Topics: genetics, gwas, popgen, pydata, statgen, statistical-genetics
• Language: Python
• Homepage: https://sgkit-dev.github.io/sgkit
• Size: 108 MB
• Stars: 275
• Watchers: 16
• Forks: 39
• Open Issues: 210
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Governance: GOVERNANCE.md

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README

          
# sgkit: Scalable genetics toolkit in Python

[![Build](https://github.com/sgkit-dev/sgkit/actions/workflows/build.yml/badge.svg)](https://github.com/sgkit-dev/sgkit/actions/workflows/build.yml)

[![Windows](https://github.com/sgkit-dev/sgkit/actions/workflows/windows.yml/badge.svg)](https://github.com/sgkit-dev/sgkit/actions/workflows/windows.yml)

[![Docs](https://github.com/sgkit-dev/sgkit/actions/workflows/docs.yml/badge.svg)](https://sgkit-dev.github.io/sgkit/)

[![Upstream](https://github.com/sgkit-dev/sgkit/actions/workflows/upstream.yml/badge.svg)](https://github.com/sgkit-dev/sgkit/actions/workflows/upstream.yml)

[![Benchmarks](https://github.com/sgkit-dev/sgkit/actions/workflows/benchmark.yml/badge.svg)](https://github.com/sgkit-dev/sgkit/actions/workflows/benchmark.yml)

[![Powered by NumFOCUS](https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](http://numfocus.org)

Sgkit is a Python package that provides a variety of analytical genetics methods through the use of

general-purpose frameworks such as [Xarray](http://xarray.pydata.org/en/stable/), [Pandas](https://pandas.pydata.org/docs/),

[Dask](https://docs.dask.org/en/latest/) and [Zarr](https://zarr.readthedocs.io/en/stable/).

For more information on using sgkit, see the [documentation](https://sgkit-dev.github.io/sgkit/).

[//]: # (numfocus-fiscal-sponsor-attribution)

The sgkit project uses a [custom governance model](./GOVERNANCE.md) 

and is fiscally sponsored by [NumFOCUS](https://numfocus.org/). Consider making 

a [tax-deductible donation](https://numfocus.org/donate-to-sgkit) to help the project 

pay for developer time, professional services, travel, workshops, and a variety of other needs.