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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 Merge branch 'master' of into whatsnew/normb…
examples update copyright years for all files touched
khmer cppcheck cleanups
lib typo, thanks @ctb
oxli updated changelog, removed bad check_space line, switched output cons…
sandbox update sandbox scripts to recent API
scripts Catch OSError too in norm-by-med ctx manager
tests converted to absolute import
third-party I have come here to chew bubblegum and delete code. And I'm all out o…
.gitattributes trying out versioneer
.gitignore Merge branch 'master' of into oxli/initial
.landscape.yaml configure service use clang's JSON compilation database for code completion
CODE_OF_CONDUCT.rst Use absolute URI in CODE_OF_CONDUCT Add link to checklist in
ChangeLog Merge pull request #1144 from dib-lab/fix/cppcheck s/Khmer /khmer /g
IDEAS remove outdated IDEAS
LICENSE Hand merge of release/update_citations slim down the PyPI distribution
Makefile cppcheck cleanups
README.rst Fix link to virtualenv install page in README.rst
TODO Add TODO item about hunting for more memory leaks.
bink.ipynb initial hacky implementation of streaming abundance binning new version 3.4.1 of comment out unneeded line from Jenkins script & document mrc additions
setup.cfg change the default test behavior to no longer stop on failed tests Revert changes added by mistake to master did merge--accidentally did other things in the middle of the merge.



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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