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In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
Python C++ Makefile Other
Branch: master
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data Correct test data for new FASTA{A,Q} name format. (Earlier conversion…
doc include 2.x release notes
examples a few more tweaks
khmer a few more tweaks
lib astyle cleanup
oxli round 2
sandbox round 2
scripts round 2
tests check EGG-INFO for scripts
third-party remove unused zlib files, doc its license
.gitattributes trying out versioneer
.gitignore Does a complete refactor of graph traversal: unifies all neighbor sea…
.landscape.yaml configure service
.mailmap update citation use clang's JSON compilation database for code completion
CITATION round 2
CODE_OF_CONDUCT.rst round 2 round 2
ChangeLog check EGG-INFO for scripts update doxygen
IDEAS remove outdated IDEAS
LICENSE remove unused zlib files, doc its license trim absent files
Makefile round 2
README.rst round 2
TODO mass renaming new version 3.4.1 of a few more tweaks
setup.cfg change the default test behavior to no longer stop on failed tests release notes for v2.0 round 2 update doxygen



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

Documentation Status PyPI Package Downloads Counter License 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:

We chat at and the maintainers can be contacted at

For getting help with 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 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

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

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