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

Research software impact Supported Python versions khmer build status Test coverage BSD-3 licensed

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:

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 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.