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.

Document Type

Article

Publication Date

6-30-2016

Notes/Citation Information

Published in Scientific Reports, v. 6, article no. 29123, p. 1-9.

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

Digital Object Identifier (DOI)

https://doi.org/10.1038/srep29123

Funding Information

These studies were funded through National Institute of Dental and Craniofacial Medicine (NIDCR) grant R01-DE022579. S.M.D. is supported by NIDCR grant T32-DE014320.

Related Content

All code for PhyloToAST is made available free and open source under the MIT license. The code is hosted on GitHub and may be downloaded at http://github.com/smdabdoub/phylotoast. Documentation of the API and all executable scripts can be found at http://docs.phylotoast.org.

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