In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
Python C++ Makefile Other
Latest commit b0404fb Oct 13, 2016 @standage standage committed on GitHub Merge pull request #1489 from dib-lab/fix/gcc_silliness
Address the silly gcc bug
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.github Updates to documentation (#1374) Jun 27, 2016
ci_scripts Adding OSX to travis Sep 2, 2016
data Correct test data for new FASTA{A,Q} name format. (Earlier conversion… Feb 20, 2013
doc update teh wrods Oct 3, 2016
examples a simple example of the C++ API (#1365) Sep 5, 2016
khmer fix copyright year Oct 2, 2016
lib make format Oct 13, 2016
oxli The style roller (#1416) Aug 31, 2016
sandbox address @standage comments Jun 27, 2016
scripts fix pep8 Oct 2, 2016
tests Make PEP8 happy Oct 4, 2016
third-party pylint fixes May 9, 2016
.dictionary pylint fixes May 9, 2016
.gitattributes trying out versioneer Oct 22, 2013
.gitignore Switch to using pytests.xml instead of nosetests.xml Aug 30, 2016
.landscape.yaml configure service Mar 2, 2014
.mailmap Replace nose with py.test (#1356) May 16, 2016
.travis.yml Undo the astyle experiment Oct 4, 2016 use clang's JSON compilation database for code completion Jun 30, 2014
CITATION Strip extraneous whitespace (#1390) Jun 23, 2016
CODE_OF_CONDUCT.rst round 2 Sep 2, 2015
ChangeLog unify format and update ChangeLog Oct 13, 2016 update doxygen Aug 14, 2015
IDEAS remove outdated IDEAS Oct 3, 2013
LICENSE remove unused zlib files, doc its license Sep 4, 2015 trim absent files Aug 14, 2015
Makefile The style roller (#1416) Aug 31, 2016
README.rst Updates to documentation (#1374) Jun 27, 2016
TODO mass renaming Aug 5, 2015 new version 3.4.1 of Apr 1, 2014 Remove temporary fix again Aug 30, 2016
pylintrc Replace nose with py.test (#1356) May 16, 2016
pytest.ini Replace nose with py.test (#1356) May 16, 2016
setup.cfg Merge branch master Jun 27, 2016 Do not link against gcov on OSX when measuring coverage Aug 30, 2016 round 2 Sep 2, 2015 versioneer 0.15+dev Oct 26, 2015


Research software impact


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