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

Research software impact

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 you can read the docs online here:

http://khmer.readthedocs.io/

There are two mailing lists dedicated to khmer, an announcements-only list and a discussion list. To search their archives and sign-up for them, please visit the following URLs:

The maintainers can be contacted at khmer-project@idyll.org.

For getting help please see this guide: http://khmer.readthedocs.io/en/stable/user/getting-help.html Your first port of call when looking for help should be: https://github.com/dib-lab/khmer/issues

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.

Install

khmer works with Python version 2.7 or 3.5. Create a virtual environemnt and install khmer with:

` pip install khmer `

You are ready to go. For more details see doc/install.rst

Contributing

If you want to modify khmer or contribute to its development read the developer instructions

License

khmer is distributed under the BSD license; see doc/LICENSE.txt. Distribution, modification and redistribution, incorporation into other software, and pretty much everything else is allowed.