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). 
`American Gut data was picked closed reference using 97% similarity in hte the greengenes 13_5 reference set.` -> `The American Gut data was picked closed reference against the greengenes 13_5 97% similarity reference set`
GreenGenes have multiple reference file, and you can use any similarity that you want with them, so it is better to specify the file used.