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khmer k-mer counting library

Project description

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

The official source code 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:

We chat at and the maintainers can be contacted at

For getting help please see this guide:


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 a 64-bit operating system and Python version 2.7.x, 3.3.x, or 3.4.x. Linux users will need the Python development libraries and gcc. OS X users may need XCode installed to build from source.

In short:

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

For more details see doc/install.rst

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.

MRC 2015-09-07

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