dib-lab/khmer — 789 Stars

dib-lab

khmer

Python

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

Last updated Jul 5, 2026

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Topics

#bioinformatics #bloom-filter #count-min-sketch #dna #graph-traversal #k-mer #python

Language breakdown

Python 70.2%

C++ 27.7%

Makefile 1.3%

Roff 0.5%

Shell 0.3%

GLSL 0.0%

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README

khmer =====

Welcome to khmer: k-mer counting, filtering, and graph traversal FTW!

The official source code repository is at https://github.com/dib-lab/khmer and project documentation is available online at http://khmer.readthedocs.io. See http://khmer.readthedocs.io/en/stable/introduction.html for an overview of the khmer project.

Getting help

See http://khmer.readthedocs.io/en/stable/user/getting-help.html for more details, but in brief:

first point of contact when looking for help:

https://github.com/dib-lab/khmer/issues

mailing list for discussion:

http://lists.idyll.org/listinfo/khmer

mailing list for announcements:

http://lists.idyll.org/listinfo/khmer-announce

email contact for project maintainers:

khmer-project@idyll.org

Important note: cite us!

khmer is research software, so you should cite us when you use it in scientific publications! Please see the CITATION <http://khmer.readthedocs.io/en/stable/citations.html>__ file for citation information.

The khmer library is a project of the Lab for Data Intensive Biology <http://ivory.idyll.org/lab/>__ at UC Davis, and includes contributions from its members, collaborators, and friends.

Quick install

pip install khmer pytest --pyargs khmer -m 'not known_failing and not jenkins and not huge and not linux'

See https://khmer.readthedocs.io/en/stable/user/install.html for more detailed installation instructions.

Contributing

We welcome contributions to khmer from the community! If you're interested in modifying khmer or contributing to its ongoing development see https://khmer.readthedocs.io/en/stable/dev/getting-started.html.

.. |Research software impact| image:: http://depsy.org/api/package/pypi/khmer/badge.svg :target: http://depsy.org/package/python/khmer .. |Supported Python versions| image:: https://img.shields.io/pypi/pyversions/khmer.svg .. |khmer build status| image:: https://img.shields.io/travis/dib-lab/khmer.svg :target: https://travis-ci.org/dib-lab/khmer .. |Test coverage| image:: https://img.shields.io/codecov/c/github/dib-lab/khmer.svg :target: https://codecov.io/github/dib-lab/khmer .. |BSD-3 licensed| image:: https://img.shields.io/badge/license-BSD%203--Clause-blue.svg :target: https://github.com/dib-lab/khmer/blob/master/LICENSE

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