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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 reorganization and fix of whats-new
examples undo load-into-{count,node}graph rename
khmer sweep of script --help output
lib remove BASHisms
oxli remove extra info()
sandbox sweep of script --help output
scripts remove unhelpful file
tests fix diff-cover & --force_single diginorm test
third-party I have come here to chew bubblegum and delete code. And I'm all out o…
.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 de-escape URL, thank you @camillescott
CODE_OF_CONDUCT.rst Use absolute URI in CODE_OF_CONDUCT Add link to checklist in
ChangeLog remove unhelpful file update doxygen
IDEAS remove outdated IDEAS
LICENSE Hand merge of release/update_citations trim absent files
Makefile fix diff-cover & --force_single diginorm test
README.rst Fix link to virtualenv install page in README.rst
TODO mass renaming
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 still need to ship oxli module fix UTF in doc/index.rst update doxygen



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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