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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 minor doc fix
examples update copyright years for all files touched
khmer fix relative imports for py3
lib Use correct lib version in OSX -current-version
oxli Merge branch 'master' of into feature/gzip505
sandbox move back to sandbox
scripts Merge branch 'master' of into feature/quiet
tests whoops, some fixes
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
.mailmap s/Jake/Jacob/g 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 branch 'master' of into feature/quiet s/Khmer /khmer /g
IDEAS remove outdated IDEAS
LICENSE Hand merge of release/update_citations include oxli script with soures; add default help
Makefile Fix test of C++ lib installation & compile
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 Only compile libary once in
setup.cfg change the default test behavior to no longer stop on failed tests Merge branch 'master' of into feature/gzip505 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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