Fig. 1

General workflow of HmmUFOtu and the default OTU-based QIIME pipeline for 16S rRNA gene sequencing studies. a Main steps of the default QIIME pipeline include: (1) generating OTUs (OTU picking); (2) selecting an individual read for each OTU as the representative sequence (rep-seq picking); (3) assigning taxonomic information to every OTU by comparing the rep-seq to the reference database (taxonomic assignment); and optionally (4) aligning rep-seqs to the references; (5) constructing a de novo OTU tree using aligned rep-seqs. b Main steps of HmmUFOtu include: (1) per-read alignment and taxonomic assignment with profile-HMM and phylogenetic placement algorithms; (2) OTU picking around existing phylogenetic nodes to generate phylogeny-based OTUs, consensus based rep-seqs, and reference-based OTU tree. Dashed circles: phylogeny-based OTUs; gray dashed lines and dots: unneeded subtrees of the reference tree that are pruned to generate the OTU tree