..
   This file is part of khmer, https://github.com/dib-lab/khmer/, and is
   Copyright (C) 2010-2015 Michigan State University
   Copyright (C) 2015 The Regents of the University of California.
   It is licensed under the three-clause BSD license; see LICENSE.
   Contact: khmer-project@idyll.org
   
   Redistribution and use in source and binary forms, with or without
   modification, are permitted provided that the following conditions are
   met:
   
    * Redistributions of source code must retain the above copyright
      notice, this list of conditions and the following disclaimer.
   
    * Redistributions in binary form must reproduce the above
      copyright notice, this list of conditions and the following
      disclaimer in the documentation and/or other materials provided
      with the distribution.
   
    * Neither the name of the Michigan State University nor the names
      of its contributors may be used to endorse or promote products
      derived from this software without specific prior written
      permission.
   
   THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
   "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
   LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
   A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
   HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
   SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
   LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
   DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
   THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
   (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
   OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
   
   Contact: khmer-project@idyll.org

khmer
=====

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

The official source code 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:

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

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

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

For getting help please see this guide: http://khmer.readthedocs.org/en/stable/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
<http://khmer.readthedocs.org/en/stable/citations.html>`__ file for
citation information.

INSTALL INSTRUCTIONS:
---------------------

khmer requires a 64-bit operating system and Python version 2.7.x, 3.3.x, or
3.4.x. Linux users will need the Python development libraries and gcc. OS X
users may need XCode installed to build from source.

In short:

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

For more details see `doc/install.rst <https://khmer.readthedocs.org/en/stable/user/install.html>`_

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 2015-09-07
