echelon9/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 source code repository is at

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

and you can read the docs online here:

http://khmer.readthedocs.io/

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

We chat at https://gitter.im/dib-lab/khmer and the maintainers can be contacted at [email protected].

For getting help please see this guide: http://khmer.readthedocs.io/en/stable/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 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 https://virtualenv.readthedocs.io/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 2015-09-07