PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets

Shareef M. Dabdoub; Megan L. Fellows; Akshay D. Paropkari; Matthew R. Mason; Sarandeep S. Huja; Alexandra A. Tsigarida; Purnima S. Kumar

doi:10.1038/srep29123

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PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets

Journal article

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PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets

Shareef M. Dabdoub, Megan L. Fellows, Akshay D. Paropkari, Matthew R. Mason, Sarandeep S. Huja, Alexandra A. Tsigarida and Purnima S. Kumar

Scientific reports, Vol.6(1), pp.29123-29123

06/30/2016

DOI: 10.1038/srep29123

PMCID: PMC4928119

PMID: 27357721

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Abstract

The 16S rRNA gene is widely used for taxonomic profiling of microbial ecosystems; and recent advances in sequencing chemistry have allowed extremely large numbers of sequences to be generated from minimal amounts of biological samples. Analysis speed and resolution of data to species-level taxa are two important factors in large-scale explorations of complex microbiomes using 16S sequencing. We present here new software, Phylogenetic Tools for Analysis of Species-level Taxa (PhyloToAST), that completely integrates with the QIIME pipeline to improve analysis speed, reduce primer bias (requiring two sequencing primers), enhance species-level analysis, and add new visualization tools. The code is free and open source, and can be accessed at http://phylotoast.org.

Multidisciplinary Sciences

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Details

Title: Subtitle: PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets
Creators: Shareef M. Dabdoub - The Ohio State University
Megan L. Fellows - The Ohio State University
Akshay D. Paropkari - The Ohio State University
Matthew R. Mason - The Ohio State University
Sarandeep S. Huja - University of Kentucky
Alexandra A. Tsigarida - University of Rochester
Purnima S. Kumar - The Ohio State University
Resource Type: Journal article
Publication Details: Scientific reports, Vol.6(1), pp.29123-29123
DOI: 10.1038/srep29123
PMID: 27357721
PMCID: PMC4928119
NLM abbreviation: Sci Rep
ISSN: 2045-2322
eISSN: 2045-2322
Publisher: Springer Nature
Number of pages: 9
Grant note: T32DE014320 / NATIONAL INSTITUTE OF DENTAL & CRANIOFACIAL RESEARCH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Dental & Craniofacial Research (NIDCR) R01-DE022579 / National Institute of Dental and Craniofacial Medicine (NIDCR) P30GM110788 / NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of General Medical Sciences (NIGMS) T32-DE014320 / NIDCR; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Dental & Craniofacial Research (NIDCR)
Language: English
Date published: 06/30/2016
Academic Unit: Dental Research; Periodontics
Record Identifier: 9984367750502771

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