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<h1> What is QIIME? <img src="home_static/images/spacer_dots.png" alt="..."></h1>
<p>
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.
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<h2> Getting started with QIIME </h2>
<p>
The quickest way to get started using QIIME is with the <a href="http://qiime.org/install/vm_ec2.html">EC2 image</a> or the <a href="http://qiime.org/install/virtual_box.html">VirtualBox</a>. The <a href="http://qiime.org/tutorials/tutorial.html">QIIME overview
tutorial</a> 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.
</p>
<p>
Before requesting help with QIIME, please review <a href="https://groups.google.com/forum/#!topic/qiime-forum/Z-KrSvdWVa4">this post</a>.</p>
<p>For getting started on interacting with the command line, please
review <a href="https://groups.google.com/forum/#!topic/qiime-forum/gs7v73s61Pg">this post</a>.</p>
<h3> Other ways to use QIIME </h3>
<p>
<a href="http://www.n3phele.com">n3phele</a>: Run QIIME on the Amazon Cloud
from a web interface - no command line interaction is required.
<br />
<a href="http://www.wernerlab.org/software/macqiime">MacQIIME</a>: Easy
install of QIIME on MacOS X.
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<h2> News </h2>
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<h2> Latest forum posts </h2>
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<h2> Most recent articles citing QIIME </h2>
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<h2>Citing QIIME<a class="headerlink" href="#citing-qiime" title="Permalink to this headline"></a></h2>
<p>If you use QIIME for any published research, please include the following citation:</p>
<blockquote>
<div>
<p><strong>QIIME allows analysis of high-throughput community sequencing data</strong>
</p>
<p>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
</p>
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</blockquote>
<p>You can find the <a class="reference external" href="http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.f.303.html">QIIME paper here</a>, and the data presented in this paper can be found
<a class="reference external" href="http://bmf.colorado.edu/QIIME/QIIME_NM_2010.tgz">here</a>.
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