An Introduction to QIIME 1.9.1

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.


This document will convert multiple major parts of python package, QIIME:

And further uses of QIIME 16s rRNA compositional data:

  • Predicted function from 16S metagenomic data (PICRUSt)
  • Linear Discriminant Analysis Effect Size (LEfSe )
  • Using MaAslin for multivariate analysis
  • Using the R-package Phyloseq for diversity analyses
  • Upload sequence data to QIITA for diversity analysis or sequence submission.

Summary of QIIME Workflow

Knight. Using QIIME to analyze 16S rRNA gene sequences from Microbial Communities: (

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