This tutorial was written to give a beginners guide of using QIIME for 16S rRNA microbial diversity analysis. It will attempt to cover a broad range of topics including, sequence processing, alpha diversity, beta diversity and taxonomic composition. All steps involve the command line and knowledge of its basic use will be an essential part of this tutorial. In this tutorial, we will use small data set to get a sense of basic commands and workflows.
Knight. Using QIIME to analyze 16S rRNA gene sequences from Microbial Communities: (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3249058/)