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).
Plugin to run the PICRUSt2 pipeline to get EC, KO, and MetaCyc pathway predictions based on 16S data. Either the default PICRUSt2 sequence placement approach or SEPP can be used to place sequences into the required reference phylogeny.
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes, and Viruses) from metagenomic shotgun sequencing data with species-level resolution.
SCNIC (Sparse Cooccurence Network Investigation for Compositional data) is a tool for building correlation networks from feature tables, finding modules in said networks and summarizing those modules. Access to all these functionalities is available to qiime2 users via the q2-SCNIC plugin.