Qiime Processing for Manuscript: Benjamino, Lincoln, Srivastava, & Graf

This repository contains the QIIME processing commands used to analyze the dataset in the manuscript titled 'Low-abundant bacteria drive compositional changes in the gut microbiota after dietary alteration' by Benjamino, Lincoln, Srivastava, and Graf. The QIIME commands are standard from QIIME 1.9 and use DictDB and Greengenes as reference databases for OTU calling.

The R script is to create an MDS plot with std. deviation ellipses.