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

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

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 p...

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Bibliographic Details
Main Authors: Qi Zheng, Casey Bartow-McKenney, Jacquelyn S. Meisel, Elizabeth A. Grice
Format: Article
Language:English
Published: BMC 2018-06-01
Series:Genome Biology
Subjects:
Microbiome
16S rRNA gene
FM-index
HMM profile alignment
Phylogenetic placement
Taxonomic assignment
Online Access:http://link.springer.com/article/10.1186/s13059-018-1450-0

Internet

http://link.springer.com/article/10.1186/s13059-018-1450-0

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