Title |
HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies
|
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Published in |
Genome Biology, June 2018
|
DOI | 10.1186/s13059-018-1450-0 |
Pubmed ID | |
Authors |
Qi Zheng, Casey Bartow-McKenney, Jacquelyn S. Meisel, Elizabeth A. Grice |
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. |
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Geographical breakdown
Country | Count | As % |
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United States | 6 | 32% |
Australia | 2 | 11% |
Japan | 1 | 5% |
China | 1 | 5% |
France | 1 | 5% |
United Kingdom | 1 | 5% |
Unknown | 7 | 37% |
Demographic breakdown
Type | Count | As % |
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Scientists | 11 | 58% |
Members of the public | 7 | 37% |
Science communicators (journalists, bloggers, editors) | 1 | 5% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 79 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 19 | 24% |
Researcher | 17 | 22% |
Student > Master | 7 | 9% |
Student > Doctoral Student | 5 | 6% |
Student > Bachelor | 5 | 6% |
Other | 15 | 19% |
Unknown | 11 | 14% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 19 | 24% |
Biochemistry, Genetics and Molecular Biology | 16 | 20% |
Immunology and Microbiology | 10 | 13% |
Computer Science | 5 | 6% |
Medicine and Dentistry | 5 | 6% |
Other | 12 | 15% |
Unknown | 12 | 15% |