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

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...

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Autores principales: Dabdoub, Shareef M., Fellows, Megan L., Paropkari, Akshay D., Mason, Matthew R., Huja, Sarandeep S., Tsigarida, Alexandra A., Kumar, Purnima S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2016
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4928119/
https://www.ncbi.nlm.nih.gov/pubmed/27357721
http://dx.doi.org/10.1038/srep29123
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author Dabdoub, Shareef M.
Fellows, Megan L.
Paropkari, Akshay D.
Mason, Matthew R.
Huja, Sarandeep S.
Tsigarida, Alexandra A.
Kumar, Purnima S.
author_facet Dabdoub, Shareef M.
Fellows, Megan L.
Paropkari, Akshay D.
Mason, Matthew R.
Huja, Sarandeep S.
Tsigarida, Alexandra A.
Kumar, Purnima S.
author_sort Dabdoub, Shareef M.
collection PubMed
description 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.
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spelling pubmed-49281192016-07-01 PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets Dabdoub, Shareef M. Fellows, Megan L. Paropkari, Akshay D. Mason, Matthew R. Huja, Sarandeep S. Tsigarida, Alexandra A. Kumar, Purnima S. Sci Rep Article 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. Nature Publishing Group 2016-06-30 /pmc/articles/PMC4928119/ /pubmed/27357721 http://dx.doi.org/10.1038/srep29123 Text en Copyright © 2016, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ 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/
spellingShingle Article
Dabdoub, Shareef M.
Fellows, Megan L.
Paropkari, Akshay D.
Mason, Matthew R.
Huja, Sarandeep S.
Tsigarida, Alexandra A.
Kumar, Purnima S.
PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets
title PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets
title_full PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets
title_fullStr PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets
title_full_unstemmed PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets
title_short PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets
title_sort phylotoast: bioinformatics tools for species-level analysis and visualization of complex microbial datasets
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4928119/
https://www.ncbi.nlm.nih.gov/pubmed/27357721
http://dx.doi.org/10.1038/srep29123
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