Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

motus - a tool for marker gene-based OTU (mOTU) profiling

bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

MaAsLin2: Microbiome Multivariate Association with Linear Models