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All Projects → dib-lab → Khmer

dib-lab / Khmer

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

Programming Languages

python
139335 projects - #7 most used programming language

Labels

bioinformaticsbloom-filterdna

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|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 <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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