This pipeline is for datasets generated from Illumina (2x300) sequencing by MR DNA. MR DNA runs sequences through a proprietary pipeline for quality control of sequences and OTU clustering. This pipeline begins with the OTU abundnace table and utilizes the representative sequence set generated by the MR DNA pipeline. Through trial and error, I have discovered the easiest and best practice for my lab is to use a combination of QIIME (full installation) and mothur. This protocol is the QIIME portion. This protocol does not include data visualization.As of 4/5/17, the following versions were used: QIIME v.1.9.1-amd64.vdi and mothur v.1.39.5