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In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
Python C++ Makefile Other
branch: master

Merge pull request #979 from lexnederbragt/test/extract_partitions_wh…


Adding a test to extract_partitions: whitespace in fasta sequence header...
latest commit b3f5379757
@mr-c mr-c authored
Failed to load latest commit information.
data Correct test data for new FASTA{A,Q} name format. (Earlier conversion…
doc @ getting-started.rst : bugfix restructuredtext.
examples automate checking of script
khmer Changelog is hard.
lib remove memory leak
sandbox update copyright
scripts Merged ged/master, addressed merge conflict, and fixed pep8 issues in…
tests Made pep8 compatible
third-party I have come here to chew bubblegum and delete code. And I'm all out o…
.gitattributes trying out versioneer
.gitignore Add PEP report files to .gitignore.
.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 ChangeLog make doc gen repro
IDEAS remove outdated IDEAS
LICENSE Hand merge of release/update_citations slim down the PyPI distribution
Makefile Fix more PEP 257 complaints; ignore missing docstrings.
README.rst changed wording of text leading up to link to GitHub issue submission
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 quiet OSX build
setup.cfg change default to \!linux in setup.cfg Fix more PEP 257 complaints; ignore missing docstrings. versioneer 0.13



Welcome to khmer: k-mer counting, filtering and graph traversal FTW!

Documentation Status PyPI Package Downloads Counter 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:

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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