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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 #788 from kdmurray91/libmakefile

./lib Makefile rewrite, create libkhmer.{a,so} and install target
latest commit 2f6e71a5f3
@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 For issue #793, fix malformed HTML/weblink syntax in changed introduc…
examples automate checking of script
khmer Merge remote-tracking branch 'ged/master' into existerror
lib Add test-compile to lib/Makefile test progs
sandbox Merge branch 'master' of into fix/sandbox_sc…
scripts future proofing: specify floor division; PEP8
tests Merge remote-tracking branch 'ged/master' into existerror
third-party Update gitignores in CPP library and 3rd party dir
.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 Document the addition of in changelog 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IDEAS remove outdated IDEAS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 Add and use it in root makefile
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 Move test of lib's make test/install to Makefile
setup.cfg change default to \!linux in setup.cfg future proofing: specify floor division; PEP8 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

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