picrust/picrust — pull request #145 by zaneveld (2013-08-31 01:45:49+00:00)
Title: Documentation for 'How PICRUSt works' and Quality Control.  Addresses Issue #126.  Addresses Issue #127. 

This is an update to the documentation.

Changes:

-- added a citation to the PICRUSt paper to the main page

-- added a 'citing PICRUSt' page that also links to other papers users may want to cite (e.g. the Werner lab's huge list of the tools drawn on by QIIME, and the ASR methods that PICRUSt uses).

-- added a 'How PICRUSt Works' page giving the rationale and some of the details for each step in genome and metagenome prediction. I'd like to add figures and formulas, but that might hold things up so that may be addressed at a later point.

-- added a 'Quality Control' section. This includes a discussion of some general limitations of PICRUSt, a list of basic quality control steps that can be undertaken for any analysis, and a brief discussion of how to use empirical sequence data as a control, as done in the paper. Finally, there is a subsection that briefly discusses a few details that might be useful to report when writing up a PICRUSt analysis, and where to look to actually find them.