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Genome Biol. 2016 May 26;17(1):111. doi: 10.1186/s13059-016-0969-1.

Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling.

Author information

1
Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
2
Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA.
3
Department of Pathology, University of Utah, Salt Lake City, UT, USA.
4
ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA.
5
Department of Pediatrics, University of Utah, Salt Lake City, UT, USA.
6
Centers for Disease Control and Prevention, Atlanta, GA, USA.
7
USTAR Center for Genetic Discovery, Salt Lake City, UT, USA.
8
Department of Human Genetics, University of Utah, Salt Lake City, UT, USA. myandell@genetics.utah.edu.
9
USTAR Center for Genetic Discovery, Salt Lake City, UT, USA. myandell@genetics.utah.edu.
10
Department of Pathology, University of Utah, Salt Lake City, UT, USA. robert.schlaberg@path.utah.edu.
11
ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA. robert.schlaberg@path.utah.edu.

Abstract

BACKGROUND:

High-throughput sequencing enables unbiased profiling of microbial communities, universal pathogen detection, and host response to infectious diseases. However, computation times and algorithmic inaccuracies have hindered adoption.

RESULTS:

We present Taxonomer, an ultrafast, web-tool for comprehensive metagenomics data analysis and interactive results visualization. Taxonomer is unique in providing integrated nucleotide and protein-based classification and simultaneous host messenger RNA (mRNA) transcript profiling. Using real-world case-studies, we show that Taxonomer detects previously unrecognized infections and reveals antiviral host mRNA expression profiles. To facilitate data-sharing across geographic distances in outbreak settings, Taxonomer is publicly available through a web-based user interface.

CONCLUSIONS:

Taxonomer enables rapid, accurate, and interactive analyses of metagenomics data on personal computers and mobile devices.

KEYWORDS:

Infectious disease diagnostics; Metagenomics; Microbiome; Pathogen detection

PMID:
27224977
PMCID:
PMC4880956
DOI:
10.1186/s13059-016-0969-1
[Indexed for MEDLINE]
Free PMC Article

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