q2-phylogenize allows users to link microbial genes to environments using phylogenetic regression. Phylogenetic regression takes into account the fact that species that share ancestry will often share phenotypic traits, including colonizing similar environments. This confounder can otherwise lead to high rates of spurious associations. We hope researchers who are doing functional analysis of 16S data will find this tool particularly useful.

A software package for learning microbe-metabolite interactions.

(pronounced /de.ko.de/) Robust Aitchison PCA for sparse omics datasets, linking specific features to beta-diversity ordination through the use of compositional biplots.

A qiime2 plugin supporting methods for geographic mapping of qiime2 artifact data or metadata.

The move from OTU-based to sOTU-based analysis, while providing additional resolution, also introduces computational challenges. We demonstrate that one popular method of dealing with sOTUs (building a de novo tree from the short sequences) can provide incorrect results in human gut metagenomic studies and show that phylogenetic placement of the new sequences with SEPP resolves this problem while also yielding other benefits over existing methods.

A QIIME 2 plugin wrapper for the SHOGUN shallow shotgun sequencing taxonomy profiler (https://github.com/knights-lab/SHOGUN).