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

被引：117

作者：

Flygare, Steven ^{[1
]}

Simmon, Keith ^{[3
]}

Miller, Chase ^{[1
]}

Qiao, Yi ^{[1
]}

Kennedy, Brett ^{[1
]}

Di Sera, Tonya ^{[1
]}

Graf, Erin H. ^{[2
]}

Tardif, Keith D. ^{[4
]}

Kapusta, Aurelie ^{[1
]}

Rynearson, Shawn ^{[1
]}

Stockmann, Chris ^{[5
]}

Queen, Krista ^{[6
]}

Tong, Suxiang ^{[6
]}

Voelkerding, Karl V. ^{[2
,4
]}

Blaschke, Anne ^{[5
]}

Byington, Carrie L. ^{[5
]}

Jain, Seema ^{[6
]}

Pavia, Andrew ^{[5
]}

Ampofo, Krow ^{[5
]}

Eilbeck, Karen ^{[3
,7
]}

Marth, Gabor ^{[1
,7
]}

Yandell, Mark ^{[1
,7
]}

Schlaberg, Robert ^{[2
,4
]}

机构：

[1] Univ Utah, Dept Human Genet, Salt Lake City, UT USA

[2] Univ Utah, Dept Pathol, Salt Lake City, UT USA

[3] Univ Utah, Dept Biomed Informat, Salt Lake City, UT USA

[4] ARUP Inst Clin & Expt Pathol, Salt Lake City, UT USA

[5] Univ Utah, Dept Pediat, Salt Lake City, UT USA

[6] Ctr Dis Control & Prevent, Atlanta, GA USA

[7] USTAR Ctr Genet Discovery, Salt Lake City, UT USA

来源：

GENOME BIOLOGY | 2016年 / 17卷

基金：

美国国家卫生研究院;

关键词：

Metagenomics; Microbiome; Pathogen detection; Infectious disease diagnostics; GUT MICROBIOTA; CONTAMINATION; CLASSIFICATION; CANCER; VIRUS; QUANTIFICATION; IDENTIFICATION; GREENGENES; DISCOVERY; DATABASE;

D O I：

10.1186/s13059-016-0969-1

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：18

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