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

Revert "Add travis config"

This reverts commit 7ad0c47.
latest commit ca55d94ede
@luizirber luizirber authored
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data Correct test data for new FASTA{A,Q} name format. (Earlier conversion…
doc Merge pull request #999 from dib-lab/doc/rev-tweak
examples update copyright years for all files touched
khmer Merge branch 'master' of into feature/labelg…
lib clean up memory leak on error exit
oxli Squash commit
sandbox renamed hashbits attribute on LabelHash to .graph; removed unnecessar…
scripts Squash commit
tests added test coverage; removed unused function
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 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 updated ChangeLog for LabelHash changes make doc gen repro
IDEAS remove outdated IDEAS
LICENSE Hand merge of release/update_citations slim down the PyPI distribution
Makefile Use FORCE in lib target of root makefile
README.rst Merge pull request #1008 from PeterDaveHello/patch-1
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 Squash commit new version of



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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