Open software for microbiome research

PICRUSt2 predicts the gene families and pathways a microbial community is likely to carry, using 16S rRNA or other marker gene sequences. It places sequences into a reference tree, infers gene content for each one, and combines the results into sample level functional profiles. The reference database was updated with PICRUSt2-SC in 2025.

A collection of standard operating procedures, tutorials and helper scripts for amplicon and shotgun metagenomic analysis, from raw reads through to taxonomic and functional profiles.

Metagenomic classifiers such as Kraken often report species that are not really present. GeCoCheck maps the reads assigned to each species back to its reference genome and uses genome coverage to separate likely true detections from false positives.

Phylogenetic Organization of Metagenomic Signals. POMS combines phylogenetic and functional data to find gene families whose distribution across the tree of life lines up with differences between sample groups.

An R package for computing contributional diversity metrics, which describe how diverse the taxa contributing to each function are, from joint taxonomic and functional profiles. It is built to run efficiently on large microbiome datasets.

An interactive visualization tool that shows which taxa contribute to each predicted function, and how those contributions differ between sample groups.