This tutorial explains how to use the QIIME (Quantitative Insights Into Microbial Ecology) Pipeline to process data from high-throughput 16S rRNA sequencing studies. If you have not already installed qiime, please see the section Installing Qiime first. The purpose of this pipeline is to provide a start-to-finish workflow, beginning with multiplexed sequence reads and finishing with taxonomic and phylogenetic profiles and comparisons of the samples in the study. With this information in hand, it is possible to determine biological and environmental factors that alter microbial community ecology in your experiment.
Here is a short/free article about advantages of QIIME.