In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
Python C++ Makefile Other
Latest commit 1745464 Nov 30, 2016 @standage standage committed on GitHub Merge pull request #1546 from dib-lab/clean_fq_to_fa
clean up ugly 'print' statement in
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.github Closes #1461. Nov 17, 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 Closes #1461. Nov 17, 2016
examples Rename CountingHash to Countgraph and Hashbits to Nodegraph (#1506) Nov 8, 2016
khmer Make pep8 happy Nov 25, 2016
legacy Merge branch "master" into luizirber-patch-1 Nov 18, 2016
lib Merge branch "master" into luizirber-patch-1 Nov 18, 2016
oxli The style roller (#1416) Aug 31, 2016
sandbox Merge branch 'master' into fix_sweep2 Nov 29, 2016
scripts clean up ugly print Nov 30, 2016
tests Create test for gzip output to stdout Nov 21, 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 Whitelist master branch for travis build-on-push Nov 14, 2016 use clang's JSON compilation database for code completion Jun 30, 2014 Changelog Nov 21, 2016
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 khmer directory cleanup Nov 15, 2016
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 move graph classes into,hh Nov 10, 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:

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.