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in-memory k-mer counting

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Merge pull request #191 from ged-lab/reservoir_sampling

A simple implementation of reservoir sampling for shotgun sequencing.
latest commit dc5c3c7f30
Camille Scott camillescott authored October 22, 2013
Octocat-spinner-32 data Merge branch 'ged-lab:master' into branch 'ged-lab:bleeding-edge'. May 13, 2013
Octocat-spinner-32 doc minor whitespace cleanup; some URL and e-mail address fixup October 14, 2013
Octocat-spinner-32 examples Added copyright headers to files August 28, 2013
Octocat-spinner-32 figuregen Added copyright headers to files August 28, 2013
Octocat-spinner-32 khmer khmer is a Python project, adopt a standard Python layout. Now that P… October 02, 2013
Octocat-spinner-32 lib move remaining legacy build options into the lib/Makefile October 07, 2013
Octocat-spinner-32 novelty Minor change in copyright header, shebang removed from a few files August 28, 2013
Octocat-spinner-32 plots Minor change in copyright header, shebang removed from a few files August 28, 2013
Octocat-spinner-32 sandbox Merge pull request #173 from ged-lab/median_count_sandbox October 14, 2013
Octocat-spinner-32 scripts added scripts/sample-reads-randomly.py, an implementation of reservoi… October 22, 2013
Octocat-spinner-32 templatem test pipeline stuff October 23, 2011
Octocat-spinner-32 tests added scripts/sample-reads-randomly.py, an implementation of reservoi… October 22, 2013
Octocat-spinner-32 .gitignore added *.egg to gitignore, to ignore side effects of 'make install' October 21, 2013
Octocat-spinner-32 ChangeLog add build changes for 0.6.1 October 15, 2013
Octocat-spinner-32 Doxyfile update doxygen to use new layout October 03, 2013
Octocat-spinner-32 IDEAS remove outdated IDEAS October 03, 2013
Octocat-spinner-32 Makefile modified 'make all' to use build_ext -i; mostly fixes ged-lab#185 October 21, 2013
Octocat-spinner-32 README.md add build status badge October 17, 2013
Octocat-spinner-32 TODO Add TODO item about hunting for more memory leaks. November 12, 2012
Octocat-spinner-32 bink.ipynb initial hacky implementation of streaming abundance binning September 01, 2013
Octocat-spinner-32 ez_setup.py khmer is a Python project, adopt a standard Python layout. Now that P… October 02, 2013
Octocat-spinner-32 jenkins-build.sh push down the cppcheck invocation from the jenkins-build script to th… October 17, 2013
Octocat-spinner-32 setup.cfg hardcode extra opts for code coverage for now October 03, 2013
Octocat-spinner-32 setup.py add build changes for 0.6.1 October 15, 2013
README.md

khmer

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

Stories in Ready Build Status

The official repository is at

https://github.com/ged-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:

You can contact the current maintainers at khmer-project@idyll.org.

IMPORTANT NOTE:

khmer is pre-publication and research software, so please keep in mind that (a) the code may have undiscovered bugs in it, (b) you should cite us, and (c) you should get in touch if you need to cite us, as we are writing up the project.

INSTALL INSTRUCTIONS:

khmer requires Python 2.7+. Linux users will need the python development libraries and gcc. OS X users will need XCode installed. For more details see doc/install.txt

In short:

pip install khmer to download, build, and install the latest stable version.

The use of a virtualenv is recommended, see http://www.virtualenv.org/en/latest/#installation

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 2013-10-07

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