In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
Python C++ Makefile Other
Latest commit a7dbf01 Feb 23, 2017 @standage standage committed on GitHub Merge pull request #1235 from dib-lab/update/expert_options
suppress display of -x and -N on argparse help
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.github Reset to master Dec 10, 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 fix counting types in python-apis Feb 14, 2017
examples Rename CountingHash to Countgraph and Hashbits to Nodegraph (#1506) Nov 8, 2016
khmer Merge branch 'master' into update/expert_options Feb 22, 2017
legacy Reset to master Dec 10, 2016
lib not a python file Feb 20, 2017
oxli consume_fasta --> consume_seqfile Feb 15, 2017
sandbox consume_fasta --> consume_seqfile Feb 15, 2017
scripts Appease pep8 Feb 15, 2017
tests Fix typo Feb 23, 2017
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 Fix generation of coverage for c++ code Feb 13, 2017 use clang's JSON compilation database for code completion Jun 30, 2014 Update Changelog Feb 20, 2017
CITATION Strip extraneous whitespace (#1390) Jun 23, 2016
CODE_OF_CONDUCT.rst round 2 Sep 2, 2015 update doxygen Aug 14, 2015
LICENSE remove unused zlib files, doc its license Sep 4, 2015 trim absent files Aug 14, 2015
Makefile Add missing header to build dependency Feb 14, 2017
README.rst Add link to issue tracker Nov 17, 2016 new version 3.4.1 of Apr 1, 2014
pylintrc Replace nose with py.test (#1356) May 16, 2016
pytest.ini Replace nose with py.test (#1356) May 16, 2016
setup.cfg Move pep8 settings to setup.cfg Nov 2, 2016 Add missing header to build dependency Feb 14, 2017 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:

The maintainers can be contacted at

For getting help please see this guide: Your first port of call when looking for help should be:

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.


khmer works with Python version 2.7 or 3.5. Create a virtual environemnt and install khmer with:

` pip install khmer `

You are ready to go. For more details see doc/install.rst


If you want to modify khmer or contribute to its development read the developer instructions


khmer is distributed under the BSD license; see doc/LICENSE.txt. Distribution, modification and redistribution, incorporation into other software, and pretty much everything else is allowed.