canido / khmer

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

khmer

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

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:

• Discussion: http://lists.idyll.org/listinfo/khmer
• Announcements: http://lists.idyll.org/listinfo/khmer-announce

You can contact the current maintainers at [email protected].

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 Python 2.7+. 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