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khmer k-mer counting library

Project description

Welcome to khmer: k-mer counting, filtering and graph traversal FTW! License Python Code Health Coverity Scan Build Status

The official repository is at

and you can read the docs online here:

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 is research software, so you should cite us when you use it in scientific publications! Please see the CITATION file for citation information.


khmer requires Python 2.7+. Linux users will need the python development libraries and gcc. OS X users may need XCode installed. For more details see doc/install.txt

In short:

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

The use of a virtualenv is recommended, see

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.

CTB 2014-03-31

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