QIIME (Quantitative Insights Into Microbial Ecology) is an open-source software pipeline for the analysis of microbiome data.



PICRUSt (Phylogenetic investigation of communities by reconstruction of unobserved states) is an open-source tool to predict metagenomic content from amplicon-based data.



BIOM (Biological Observation Matrix) is a standard to represent rich contingency tables, such as OTU tables generated from 16S rRNA gene sequencing but also metagenome or metabolomic tables.