Toward fully reproducible microbiome multi-omics bioinformatics with QIIME 2

About this Class

https://cap-lab.bio(link is external)

https://(link is external)qiime2.org(link is external)

The QIIME platform, including QIIME 1 and QIIME 2 (https://qiime2.org(link is external)), has been extensively applied in microbiome research, repeatedly making analyses that were once challenging or impossible into routine tasks. While QIIME began as a marker gene (e.g., 16S, ITS, ...) analysis platform, microbiome research is rapidly transitioning toward multi-omics data, introducing many new informatics challenges. With funding from NCI’s Informatics Technology for Cancer Research program (https://itcr.cancer.gov/), QIIME 2 is transitioning to become a microbiome multi-omics data science platform. 

In this talk I will introduce QIIME 2, including our current work on expanding beyond marker gene analysis, including the new QIIME 2 Shotgun Metagenomics Distribution. I will also discuss QIIME 2’s retrospective data provenance tracking system, including our recently introduced Provenance Replay functionality (https://doi.org/10.1371/journal.pcbi.1011676(link is external)), which enables you to automatically generated new code from your existing QIIME 2 results to reproduce and "replay" analyses that you or others ran. I will describe the ways that QIIME 2 can be used, including through the Galaxy graphical user interface (https://cancer.usegalaxy.org(link is external)), its command line interface, and its 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 (https://doi.org/10.1371/journal.pcbi.1009056(link is external)) so you can start learning and applying QIIME 2 to advance your work as quickly as possible.