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update the front page documentation #1267

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update the front page documentation #1267

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d87b4e8
update intro and biblio
ctb Aug 18, 2015
dc2548b
update ChangeLog
ctb Aug 18, 2015
8747802
reference new location of base CSS
mr-c Aug 18, 2015
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6 changes: 6 additions & 0 deletions ChangeLog
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2015-08-18 Titus Brown <titus@idyll.org>

* doc/index.rst: update introductory text.
* doc/user/biblio.rst: update bibliography link descriptions and text.
* doc/_static/labibi.css: reference new location of base CSS

2015-08-14 Luiz Irber <khmer@luizirber.org>

* scripts/unique-kmers.py: Rename option --stream-out to --stream-records.
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2 changes: 1 addition & 1 deletion doc/_static/labibi.css
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@import url('default.css');
@import url('classic.css');

/* Styles for floating Edit on GitHub box */
#editor-trap {
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84 changes: 57 additions & 27 deletions doc/index.rst
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.. vim: set filetype=rst

#######################################
khmer -- k-mer counting & filtering FTW
#######################################
###################################################################
The khmer software for advanced biological sequencing data analysis
###################################################################

What is khmer?
==============

The khmer software is a set of command-line tools for working with DNA
shotgun sequencing data from genomes, transcriptomes, metagenomes, and
single cells. khmer can make *de novo* assemblies faster, and
sometimes better. khmer can also identify (and fix) problems with
shotgun data. You can read more about khmer in `our software paper
<https://dx.doi.org/10.12688/f1000research.6924.1>`__.

khmer is free and open source software.

**To install khmer**, you will need a Linux or Mac computer, together with
Python 2.7 or Python 3.x. See `our installation docs <user/install.html>`__
for detailed instructions.

**To use khmer**, you will generally need to work at the UNIX command
line. See `our command line documentation <user/scripts.html>`__.

We have **additional documentation** in several places, including
`protocols for metagenome and mRNAseq assembly
<https://khmer-protocols.readthedocs.org/>`__ and `recipes for several
common research tasks <https://khmer-recipes.readthedocs.org/>`__.
You might also be interested in `papers using or citing khmer
<user/biblio.html>`__.

**To get help**, please ask questions on `the khmer mailing list
<http://lists.idyll.org/listinfo/khmer>`__ or `post an issue on
GitHub <https://github.com/dib-lab/khmer/issues/new>`__.

We welcome contributions to the khmer project! We are friendly and
supportive of new contributors, and have a `code of conduct
<dev/CODE_OF_CONDUCT.html>`__. Please see our `docs on getting
started on khmer development <dev/getting-started.html>`__.

Details
=======

:Authors: Michael R. Crusoe, Hussien F. Alameldin, Sherine Awad, Elmar
Bucher, Adam Caldwell, Reed Cartwright, Amanda Charbonneau, Bede
Expand All @@ -25,15 +63,18 @@ khmer -- k-mer counting & filtering FTW
:Chat: https://gitter.im/dib-lab/khmer
:License: BSD

.. toctree::
:maxdepth: 1

khmer is a library and suite of command line tools for working with
DNA sequences. 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.

:doc:`user/install`

:doc:`user/getting-help`
introduction
contributors
citations
whats-new-2.0
release-notes/index
user/index
dev/index
roadmap
LICENSE

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
Expand All @@ -46,23 +87,12 @@ the following URLs:
The archives for the khmer mailing list are available at:
http://lists.idyll.org/pipermail/khmer/

khmer development has largely been supported by AFRI Competitive Grant
khmer development was initially 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>`__ through
May 2016, both to C. Titus Brown.

.. toctree::
:maxdepth: 1

introduction
contributors
citations
whats-new-2.0
release-notes/index
user/index
dev/index
roadmap
LICENSE
`R01HG007513 <http://ged.msu.edu/downloads/2012-bigdata-nsf.pdf>`__
through May 2016, both to C. Titus Brown. More recently, we have
received support from the Gordon and Betty Moore Foundation under
Award number GBMF4551.
35 changes: 16 additions & 19 deletions doc/user/biblio.rst
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An incomplete bibliography of papers using khmer
================================================
Papers using khmer
==================

khmer was first published in `Scaling metagenome sequence assembly
with probabilistic de Bruijn graphs, Pell et al., 2012
<http://www.pnas.org/content/109/33/13272.full>`__.

Since then, we have `published several additional papers
<http://www.ncbi.nlm.nih.gov/sites/myncbi/1ruvipqAmaMkN/collections/48107445/public/>`__.

Please also see `the instructions for citing our papers and software
<https://github.com/dib-lab/khmer/blob/master/CITATION>`__.

Biological uses outside of the group
------------------------------------

http://www.ncbi.nlm.nih.gov/sites/myncbi/1ruvipqAmaMkN/collections/48107393/public/
See `this list of papers <http://www.ncbi.nlm.nih.gov/sites/myncbi/1ruvipqAmaMkN/collections/48107393/public/>`__ for publications using khmer to analyze
their sequencing data.

Tools building on khmer concepts
--------------------------------

http://www.ncbi.nlm.nih.gov/sites/myncbi/1ruvipqAmaMkN/collections/48101567/public/

Papers in collaboration with our group
--------------------------------------

http://www.ncbi.nlm.nih.gov/sites/myncbi/1ruvipqAmaMkN/collections/48107445/public/

Digital normalization
---------------------

Multiple Single-Cell Genomes Provide Insight into Functions of
Uncultured Deltaproteobacteria in the Human Oral Cavity. Campbell et
al., PLoS One, 2013, doi:10.1371/journal.pone.0059361. [ `paper link
<http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0059361>`__ ]


Several `research papers
<http://www.ncbi.nlm.nih.gov/sites/myncbi/1ruvipqAmaMkN/collections/48101567/public/>`__
have built off of concepts introduced in or elaborated on khmer.