Overview of data generation, processing and analysis using QIIME

Overview of data generation, processing and analysis workflow using QIIME (or other similar packages). After DNA is extracted, a target region (e.g. part of the 16S or 18S rRNA gene) is amplified using error-correcting, Golay barcoded primers (barcodes noted by sequences of different colors). Next, the multiplexed pool of amplicons is sequenced at a depth of millions of sequences. Finally, the open-access software package QIIME is used to demultiplex sequences, align sequences to the reference database (e.g. Greengenes or SILVA), and perform statistical analyses and generate visualizations (e.g. ANOSIM and PCoA plots). This schematic is based on a figure originally published in Hamady et al. 2008 and updated by J. Metcalf, J.G. Caporaso, M.Pirrung, and R. Knight. This figure is available at Figshare.com under the open-access Creative Commons-Attribution License (CC-BY).

Hamady M, Knight R (2009) Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Research 19, 1141-1152.