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

Flygare, Steven; Simmon, Keith; Miller, Chase; Qiao, Yi; Kennedy, Brett; Di Sera, Tonya; Graf, Erin H.; Tardif, Keith D.; Kapusta, Aurélie; Rynearson, Shawn; Stockmann, Chris; Queen, Krista; Tong, Suxiang; Voelkerding, Karl V.; Blaschke, Anne; Byington, Carrie L.; Jain, Seema; Pavia, Andrew; Ampofo, Krow; Eilbeck, Karen; Marth, Gabor; Yandell, Mark; Schlaberg, Robert

doi:10.1186/s13059-016-0969-1

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

Published Date:

May 26 2016

Publisher's site:

http://dx.doi.org/10.1186/s13059-016-0969-1 New Site Icon

Source:

Genome Biol. 17.

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

Details:

Alternative Title:

Genome Biol

Personal Author:

Flygare, Steven ; Simmon, Keith ; Miller, Chase ; Qiao, Yi ; Kennedy, Brett ; ... More ▼

Description:

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.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-016-0969-1) contains supplementary material, which is available to authorized users.

Subject:

[+]

Pubmed ID:

27224977

Pubmed Central ID:

PMC4880956

Document Type:

Journal Article

Collection(s):

CDC Public Access

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