Preprocessing

The preprocessing notebook for the American Gut data. A version of the notebook text can be found on [google docs](https://docs.google.com/document/d/1AR2GrHsVT8LjVTiRHPnn43GF_Eoz8wT5ZH3Q-Of9-BI/edit?usp=sharing). 
But QIIME 1.8 is not compatible with BIOM 2.x, and this code is using the BIOM 2.x API. It's relatively minor, but everything else we produce now is HDF5