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HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies. | LitMetric

HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies.

Genome Biol

Department of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Blvd, BRB 1046/7, Philadelphia, PA, 19104, USA.

Published: June 2018

AI Article Synopsis

Article Abstract

Culture-independent analysis of microbial communities frequently relies on amplification and sequencing of the prokaryotic 16S ribosomal RNA gene. Typical analysis pipelines group sequences into operational taxonomic units (OTUs) to infer taxonomic and phylogenetic relationships. Here, we present HmmUFOtu, a novel tool for processing microbiome amplicon sequencing data, which performs rapid per-read phylogenetic placement, followed by phylogenetically informed clustering into OTUs and taxonomy assignment. Compared to standard pipelines, HmmUFOtu more accurately and reliably recapitulates microbial community diversity and composition in simulated and real datasets without relying on heuristics or sacrificing speed or accuracy.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6020470PMC
http://dx.doi.org/10.1186/s13059-018-1450-0DOI Listing

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