In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
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Research software impact Supported Python versions khmer build status Test coverage BSD-3 licensed


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

The official source code repository is at and project documentation is available online at See for an overview of the khmer project.

Getting help

See for more details, but in brief:

Important note: cite us!

khmer is research software, so you should cite us when you use it in scientific publications! Please see the CITATION file for citation information.

The khmer library is a project of the Lab for Data Intensive Biology 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 for more detailed installation instructions.


We welcome contributions to khmer from the community! If you're interested in modifying khmer or contributing to its ongoing development see