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

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
https://github.com/dib-lab/khmer

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

Last synced: 4 days ago
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In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

• Host: GitHub
• URL: https://github.com/dib-lab/khmer
• Owner: dib-lab
• License: other
• Created: 2012-05-15T03:52:53.000Z (over 13 years ago)
• Default Branch: master
• Last Pushed: 2024-02-17T11:37:33.000Z (almost 2 years ago)
• Last Synced: 2026-01-18T03:51:10.836Z (5 days ago)
• Topics: bioinformatics, bloom-filter, count-min-sketch, dna, graph-traversal, k-mer, python
• Language: Python
• Homepage: http://khmer.readthedocs.io/
• Size: 50.4 MB
• Stars: 783
• Watchers: 67
• Forks: 297
• Open Issues: 353
• Metadata Files:
  • Readme: README.rst
  • Changelog: CHANGELOG.md
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.rst
  • Citation: CITATION
  • Authors: authors.csv

Awesome Lists containing this project

• awesome-scientific-python - khmer - k-mer counting, filtering, and graph traversal. (Domain-specific libraries / Bioinformatics)

README

          
|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:

-  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 `__ 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.

.. |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