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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 #1157 from dib-lab/fix/python3_errors

Fix Python 3 errors and coding style
latest commit 873f6ffe53
@mr-c mr-c authored
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data Correct test data for new FASTA{A,Q} name format. (Earlier conversion…
doc Merge branch 'master' of github.com:ged-lab/khmer into whatsnew/normb…
examples update copyright years for all files touched
khmer cppcheck cleanups
lib make format
oxli make format
sandbox Replace xrange and cStringIO
scripts Catch OSError too in norm-by-med ctx manager
tests make format
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 github.com:ged-lab/khmer into oxli/initial
.landscape.yaml configure landscape.io service
.ycm_extra_conf.py use clang's JSON compilation database for code completion
CITATION s=github.com/ged-lab=github.com/dib-lab=g
CODE_OF_CONDUCT.rst Use absolute URI in CODE_OF_CONDUCT
CONTRIBUTING.md Add link to checklist in CONTRIBUTING.md
ChangeLog Add ChangeLog
Doxyfile.in s/Khmer /khmer /g
IDEAS remove outdated IDEAS
LICENSE Hand merge of release/update_citations
MANIFEST.in slim down the PyPI distribution
Makefile cppcheck cleanups
README.rst Fix link to virtualenv install page in README.rst
TODO Add TODO item about hunting for more memory leaks.
bink.ipynb initial hacky implementation of streaming abundance binning
ez_setup.py new version 3.4.1 of ez_setup.py
jenkins-build.sh comment out unneeded line from Jenkins script & document mrc additions
setup.cfg change the default test behavior to no longer stop on failed tests
setup.py Revert changes added by mistake to master
versioneer.py did merge--accidentally did other things in the middle of the merge.

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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