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In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
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data Correct test data for new FASTA{A,Q} name format. (Earlier conversion…
doc include 2.x release notes
examples a few more tweaks
khmer a few more tweaks
lib astyle cleanup
oxli round 2
sandbox round 2
scripts round 2
tests check EGG-INFO for scripts
third-party remove unused zlib files, doc its license
.gitattributes trying out versioneer
.gitignore Does a complete refactor of graph traversal: unifies all neighbor sea…
.landscape.yaml configure landscape.io service
.mailmap update citation
.ycm_extra_conf.py use clang's JSON compilation database for code completion
CITATION round 2
CODE_OF_CONDUCT.rst round 2
CONTRIBUTING.md round 2
ChangeLog check EGG-INFO for scripts
Doxyfile.in update doxygen
IDEAS remove outdated IDEAS
LICENSE remove unused zlib files, doc its license
MANIFEST.in trim absent files
Makefile round 2
README.rst round 2
TODO mass renaming
ez_setup.py new version 3.4.1 of ez_setup.py
jenkins-build.sh a few more tweaks
setup.cfg change the default test behavior to no longer stop on failed tests
setup.py release notes for v2.0
sort-authors-list.py round 2
versioneer.py update doxygen

README.rst

khmer

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

Documentation Status PyPI Package Downloads Counter License http://ci.ged.msu.edu/job/khmer-master/badge/icon Coverity Scan Build Status

The official repository is at

https://github.com/dib-lab/khmer

and you can read the docs online here:

http://khmer.readthedocs.org/

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 https://gitter.im/dib-lab/khmer and the maintainers can be contacted at khmer-project@idyll.org.

For getting help with please see this guide: http://khmer.readthedocs.org/user/getting-help.html

IMPORTANT NOTE: CITE US!

khmer is research software, so you should cite us when you use it in scientific publications! Please see the CITATION file for citation information.

INSTALL INSTRUCTIONS:

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 https://virtualenv.readthedocs.org/en/latest/installation.html

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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