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In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
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Latest commit e6eed56 @ctb ctb Merge pull request #1329 from dib-lab/fix/1328
Check iterator before decrementing on repartition_largest_partition
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data Correct test data for new FASTA{A,Q} name format. (Earlier conversion…
doc refresh for 2.0
examples a few more tweaks
khmer update magic; add IANA approved media type
lib Check iterator before decrementing
oxli round 2
sandbox added executable bit to sandbox/
scripts fix and test for close of --output file after first input file
tests fix and test for close of --output file after first input file
third-party remove unused zlib files, doc its license
.gitattributes trying out versioneer
.gitignore Does a complete refactor of graph traversal: unifies all neighbor sea…
.landscape.yaml configure service
.mailmap update citation use clang's JSON compilation database for code completion
CITATION round 2
CODE_OF_CONDUCT.rst round 2 round 2
ChangeLog Add ChangeLog entry update doxygen
IDEAS remove outdated IDEAS
LICENSE remove unused zlib files, doc its license trim absent files
Makefile round 2
README.rst refresh for 2.0
TODO mass renaming new version 3.4.1 of a few more tweaks
setup.cfg change the default test behavior to no longer stop on failed tests release notes for v2.0 round 2 update doxygen



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

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