This tutorial covers a full QIIME workflow using Illumina sequencing data and was adapted from a tutorial on the QIIME website.. This tutorial is intended to be quick to run, and as such, uses only a subset of a full Illumina Genome Analyzer II (GAIIx) run. We'll make use of the Greengenes reference OTUs, which is the default reference database used by QIIME. You can determine which version of Greengenes is being used by running print_qiime_config.py. This will be Greengenes, unless you've configured QIIME to use a different reference database by default.The data used in this tutorial are derived from the Moving Pictures of the Human Microbiome study, where two human subjects collected daily samples from four body sites: the tongue, the palm of the left hand, the palm of the right hand, and the gut (via fecal samples obtained by swapping used toilet paper). These data were sequenced using the barcoded amplicon sequencing protocol described in Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. A more recent version of this protocol that can be used with the Illumina HiSeq 2000 and MiSeq can be found here.