What is QIIME?

QIIME (pronounced "chime") stands for Quantitative Insights Into Microbial Ecology. QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data). QIIME takes users from their raw sequencing output through initial analyses such as OTU picking, taxonomic assignment, and construction of phylogenetic trees from representative sequences of OTUs, and through downstream statistical analysis, visualization, and production of publication-quality graphics. QIIME has been applied to single studies based on billions of sequences from thousands of samples.

Getting started with QIIME

The quickest way to get started using QIIME is with the EC2 image or the VirtualBox. The QIIME overview tutorial is a good first analysis to run. In this tutorial you'll download a small data set and work through a series of commands that will introduce you to QIIME's most commonly used features and analyses.

Before requesting help with QIIME, please review this post.

For getting started on interacting with the command line, please review this post.

Other ways to use QIIME

n3phele: Run QIIME on the Amazon Cloud from a web interface - no command line interaction is required.
MacQIIME: Easy install of QIIME on MacOS X.

News

Latest forum posts

Most recent articles citing QIIME

Citing QIIME

If you use QIIME for any published research, please include the following citation:

QIIME allows analysis of high-throughput community sequencing data

J Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, Antonio Gonzalez Pena, Julia K Goodrich, Jeffrey I Gordon, Gavin A Huttley, Scott T Kelley, Dan Knights, Jeremy E Koenig, Ruth E Ley, Catherine A Lozupone, Daniel McDonald, Brian D Muegge, Meg Pirrung, Jens Reeder, Joel R Sevinsky, Peter J Turnbaugh, William A Walters, Jeremy Widmann, Tanya Yatsunenko, Jesse Zaneveld and Rob Knight; Nature Methods, 2010; doi:10.1038/nmeth.f.303

You can find the QIIME paper here, and the data presented in this paper can be found here.