Skip to content
/ khmer Public

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

License

Notifications You must be signed in to change notification settings

dib-lab/khmer

Folders and files

NameName
Last commit message
Last commit date

Latest commit

9fd52c9 · Jul 20, 2015
Feb 20, 2013
Jul 5, 2015
May 15, 2015
Jul 20, 2015
Jul 17, 2015
Jul 19, 2015
Jul 19, 2015
Jul 19, 2015
Jul 19, 2015
Apr 1, 2015
Oct 22, 2013
May 20, 2015
Mar 2, 2014
Jun 30, 2014
May 15, 2015
Dec 8, 2014
Feb 3, 2015
Jul 18, 2015
Jun 17, 2015
Oct 3, 2013
Apr 1, 2014
Jun 13, 2014
Jul 17, 2015
Jun 27, 2015
Nov 12, 2012
Sep 1, 2013
Apr 1, 2014
Jun 13, 2015
Jun 30, 2015
Jun 12, 2015
Jun 12, 2015

Repository files navigation

khmer

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

Documentation Status PyPI Package Downloads Counter License http://ci.ged.msu.edu/job/khmer-master/badge/icon Coverity Scan Build Status

The official repository is at

https://github.com/dib-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:

We chat at https://gitter.im/dib-lab/khmer and the maintainers can be contacted at khmer-project@idyll.org.

For getting help with please see this guide: http://khmer.readthedocs.org/user/getting-help.html

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.readthedocs.org/en/latest/installation.html

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 2014-05-14