Associate Professor Greg Caporaso

Reproducible and accessible microbiome multi-omics analysis with QIIME 2

The QIIME platform, including QIIME 1 and QIIME 2, has been extensively applied in microbiome research, repeatedly making analyses that were challenging or impossible into routine tasks. While QIIME began as a marker gene (e.g., 16S, ITS, …) analysis platform, microbiome research is transitioning toward multi-omics. With funding from NCI’s Informatics Technology for Cancer Research program, QIIME 2 is transitioning to become a microbiome multi-omics analysis platform. In this talk I will introduce QIIME 2, including our current work on expanding beyond marker gene analysis. I will also discuss QIIME 2’s retrospective data provenance tracking system, and how it can help you to get help with your bioinformatics analyses and ensure that your work is reproducible. I will describe the ways that QIIME 2 can be used, including through the Galaxy graphical user interface, a command line interface, or a Python 3 API. Full support for using QIIME 2 through these different interface types ensures that using QIIME 2 will be accessible and convenient for you, regardless of your computational background. Finally, I’ll present on QIIME 2’s extensive educational and technical support resources so you can start learning QIIME 2 as quickly as possible.

Dr Greg Caporaso

Associate Professor, Northern Arizona University

Dr. Greg Caporaso is an Associate Professor at Northern Arizona University. He is a microbiome expert, having published over 100 papers on the human microbiome, environmental microbiomes, and microbiome bioinformatics. He leads the development of the popular QIIME microbiome bioinformatics platform (, a very widely used tool in microbiome research which has been cited over 30,000 times since its initial publication in 2009, and is regularly involved in teaching QIIME 2, bioinformatics, and scientific computing. Dr. Caporaso’s lab website can be found at