.. khmer documentation master file, created by
   sphinx-quickstart on Wed Aug  4 10:20:23 2010.
   You can adapt this file completely to your liking, but it should at least
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khmer -- k-mer counting & filtering FTW
=======================================

:Authors: Michael R. Crusoe, Greg Edvenson, Jordan Fish, Adina Howe,
Eric McDonald, Joshua Nahum, Kaben Nanlohy, Jason Pell, Jared Simpson,
C. S. Welcher, Qingpeng Zhang, and C. Titus Brown
:Contact: ctb@msu.edu
:License: BSD

khmer is a library and suite of command line tools for working with
DNA sequence.  It is primarily aimed at short-read sequencing data
such as that produced by the Illumina platform.  khmer takes a k-mer-centric
approach to sequence analysis, hence the name.

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:
    
    * Discussion: http://lists.idyll.org/listinfo/khmer

    * Announcements: http://lists.idyll.org/listinfo/khmer-announce

The archives for the khmer list are available at: http://lists.idyll.org/pipermail/khmer/

khmer development has largely been supported by AFRI Competitive Grant
no.  `2010-65205-20361
<http://ged.msu.edu/downloads/2009-usda-vertex.pdf>`__ from the USDA
NIFA, and is now funded by the National Human Genome Research
Institute of the National Institutes of Health under Award Number
`R01HG007513 <http://ged.msu.edu/downloads/2012-bigdata-nsf.pdf>`__,
both to C. Titus Brown.

Contents:

.. toctree::
   :maxdepth: 1

   introduction
   install
   examples
   guide
   scripts
   blog-posts
   choosing-hash-sizes
   partitioning-big-data
   ktable
   design
   details
   development
   crazy-ideas
   contributors
   biblio

   LICENSE

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

