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

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README.rst

khmer

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

https://badge.fury.io/py/khmer.png https://pypip.in/d/khmer/badge.png License http://ci.ged.msu.edu/job/khmer-master/badge/icon Python Code Health Coverity Scan Build Status

The official repository is at

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

and you can read the docs online here:

http://khmer.readthedocs.org/

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:

You can contact the current maintainers at 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.

INSTALL INSTRUCTIONS:

khmer requires a 64-bit operating system and Python 2.7.x. Linux users will need the Python development libraries and gcc. OS X users may need XCode installed.

In short:

pip install khmer to download, build, and install the latest stable version.

For more details see doc/install.txt

The use of a virtualenv is recommended, see https://virtualenv.pypa.io/en/latest/virtualenv.html#installation

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

khmer project contributors also edit documents collaboratively at our wiki.

MRC 2014-05-14

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