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index.txt
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===============
khmer protocols
===============
:version: 0.8.5 (unreleased)
This is a set of protocols for doing genomic data analysis -- specifically,
de novo mRNAseq assembly and de novo metagenome assembly -- in the cloud.
The latest released version of these protocols can always be found
at:
http://khmer-protocols.readthedocs.org/
.. You are reading v0.8.5; please use the following URL in citations and
.. discussions:
.. https://khmer-protocols.readthedocs.org/en/v0.8.5/
If you need to reference these protocols, please cite::
Brown, C. Titus; Sheneman, Leigh; Scott, Camille; Crusoe, Michael;
Rosenthal, Josh; Howe, Adina Chuang (2013): khmer-protocols
documentation.
figshare. http://dx.doi.org/10.6084/m9.figshare.878460
Helpful instructions:
---------------------
* :doc:`amazon/index` -- information on Amazon instances
* :doc:`../docs/command-line` -- command-line conventions for the khmer protocols
Protocols:
----------
mRNAseq assembly: the Eel Pond Protocol
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:doc:`mrnaseq/index`
This is a lightweight protocol for assembling up to a few hundred
million mRNAseq reads, annotating the resulting assembly, and doing
differential expression with RSEM.
Metagenome assembly: the Kalamazoo Protocol
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:doc:`metagenomics/index`
This is a protocol for assembling low- and medium-diversity metagenomes.
Marine sediment and soil data sets may not be assemblable in the cloud
just yet.
Additional information
----------------------
Need help? Either post comments on the bottom of each page, OR
`sign up for the mailing list <http://lists.idyll.org/listinfo/protocols>`__.
Have you used these protocols in a scientific publication? We'll have
citation instructions up soon.
Funding
-------
khmer-protocols 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 Award Number `R25HG006243
<http://ged.msu.edu/downloads/2010-ngs-course-nih-r25.pdf>`__ from the
National Institutes of Health, both to C. Titus Brown.
We now have continuing support from
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>`__,
also to C. Titus Brown.
CTB's work on the Eel Pond mRNAseq tutorial was enabled by his 2013 summer
research work at `the Marine Biological Laboratory
<http://www.mbl.edu>`__, funded by the Burr and Susie Steinbach Award
and the Laura and Arthur Colwin Endowed Summer Research Fellowship
Fund
TODO:
-----
* remove/transition stuff from the angus site.
* add sfg/stanford: http://sfg.stanford.edu/
* send to biostar-ninjas