Skip to content


Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
branch: master
Failed to load latest commit information.
data Correct test data for new FASTA{A,Q} name format. (Earlier conversion…
doc Fixed missed ChangeLog merge conflicts, updated doc link
examples automate checking of script
khmer Merge pull request #738 from ged-lab/tests/hll_coverage
lib Additional tests and checks
sandbox update changelog
scripts Merge branch 'master' of into fix/csv_count-…
tests Update
third-party Change type in MurmurHash3 and _revcomp
.gitattributes trying out versioneer
.gitignore Removed cruft identified by pylint
.landscape.yaml configure service use clang's JSON compilation database for code completion
CITATION don't list specific SeqAn scripts
CODE_OF_CONDUCT.rst Use absolute URI in CODE_OF_CONDUCT Add link to checklist in
ChangeLog Merge branch 'master' of into fix/csv_count-… Resolved missed merge conflicts. Updated formatting. Made mental notes.
IDEAS remove outdated IDEAS
LICENSE Hand merge of release/update_citations slim down the PyPI distribution
Makefile only run the new tests on Linux
README.rst clarify py version req
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 remove examples/stamps testing for now
setup.cfg change default to \!linux in setup.cfg Add missing header to BUILD_DEPENDS versioneer update



Welcome to khmer: k-mer counting, filtering and graph traversal FTW! License Python Code Health 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:

You can contact the current maintainers at


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.

khmer project contributors also edit documents collaboratively at our wiki.

MRC 2014-05-14

Something went wrong with that request. Please try again.