initial module 2 processing template
readded file details
ignore contested strings
Merge pull request #55 from wasade/ignore_contested_taxstrings

ignore contested strings
addressing comments
Merge branch 'master' of github.com:qiime/American-Gut into mod2
added one link, fixed broken json
Merge pull request #53 from wasade/mod2

initial module 2 processing template
New latex template for oral and skin.  Reorganized latex directory.
Cleaning up deleted files.
Merge pull request #57 from cuttlefishh/skin-oral-1

New latex template for oral and skin.  Reorganized latex directory.
Merge branch 'filtering_notebook' of github.com:adamrp/American-Gut into filtering_notebook
Most recent notebook for filtering

This will likely change soon as we find a better way to find the threshold
that is used to identify contaminant sequences in an OTU.  Currently, the
threshold is set to 90%; if a single sequence composes >=90% of the over-
represented gammaproteo OTU, then the sequence is labeled as a contaminant.
Instead, we would like to define this threshold based on the sequencing
error rate as determined by the Illumina instrument.