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

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

doi:10.1186/s13059-016-0969-1

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

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

Academic Institute

Research output: Contribution to journal › Article › peer-review

132 Scopus citations

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.

Original language	English (US)
Article number	111
Journal	Genome Biology
Volume	17
Issue number	1
DOIs	https://doi.org/10.1186/s13059-016-0969-1
State	Published - May 26 2016

Keywords

Infectious disease diagnostics
Metagenomics
Microbiome
Pathogen detection

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

Access to Document

10.1186/s13059-016-0969-1

Cite this

Flygare, S., Simmon, K., Miller, C., Qiao, Y., Kennedy, B., Di Sera, T., Graf, E. H., Tardif, K. D., Kapusta, A., Rynearson, S., Stockmann, C., Queen, K., Tong, S., Voelkerding, K. V., Blaschke, A., Byington, C. L., Jain, S., Pavia, A., Ampofo, K., ... Schlaberg, R. (2016). Taxonomer: An interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling. Genome Biology, 17(1), Article 111. https://doi.org/10.1186/s13059-016-0969-1

Flygare, S, Simmon, K, Miller, C, Qiao, Y, Kennedy, B, Di Sera, T, Graf, EH, Tardif, KD, Kapusta, A, Rynearson, S, Stockmann, C, Queen, K, Tong, S, Voelkerding, KV, Blaschke, A, Byington, CL, Jain, S, Pavia, A, Ampofo, K, Eilbeck, K, Marth, G, Yandell, M & Schlaberg, R 2016, 'Taxonomer: An interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling', Genome Biology, vol. 17, no. 1, 111. https://doi.org/10.1186/s13059-016-0969-1

@article{65d150ddf7b742f589c4cfcdfa784b4a,

title = "Taxonomer: An interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling",

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",

author = "Steven Flygare and Keith Simmon and Chase Miller and Yi Qiao and Brett Kennedy and {Di Sera}, Tonya and Graf, {Erin H.} and Tardif, {Keith D.} and Aur{\'e}lie Kapusta and Shawn Rynearson and Chris Stockmann and Krista Queen and Suxiang Tong and Voelkerding, {Karl V.} and Anne Blaschke and Byington, {Carrie L.} and Seema Jain and Andrew Pavia and Krow Ampofo and Karen Eilbeck and Gabor Marth and Mark Yandell and Robert Schlaberg",

note = "Publisher Copyright: {\textcopyright} 2016 Flygare et al.",

year = "2016",

month = may,

day = "26",

doi = "10.1186/s13059-016-0969-1",

language = "English (US)",

volume = "17",

journal = "Genome Biology",

issn = "1474-7596",

publisher = "BioMed Central Ltd.",

number = "1",

}

TY - JOUR

T1 - Taxonomer

T2 - An interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling

AU - Flygare, Steven

AU - Simmon, Keith

AU - Miller, Chase

AU - Qiao, Yi

AU - Kennedy, Brett

AU - Di Sera, Tonya

AU - Graf, Erin H.

AU - Tardif, Keith D.

AU - Kapusta, Aurélie

AU - Rynearson, Shawn

AU - Stockmann, Chris

AU - Queen, Krista

AU - Tong, Suxiang

AU - Voelkerding, Karl V.

AU - Blaschke, Anne

AU - Byington, Carrie L.

AU - Jain, Seema

AU - Pavia, Andrew

AU - Ampofo, Krow

AU - Eilbeck, Karen

AU - Marth, Gabor

AU - Yandell, Mark

AU - Schlaberg, Robert

PY - 2016/5/26

Y1 - 2016/5/26

N2 - 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.

AB - 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.

KW - Infectious disease diagnostics

KW - Metagenomics

KW - Microbiome

KW - Pathogen detection

UR - http://www.scopus.com/inward/record.url?scp=84969961419&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84969961419&partnerID=8YFLogxK

U2 - 10.1186/s13059-016-0969-1

DO - 10.1186/s13059-016-0969-1

M3 - Article

C2 - 27224977

AN - SCOPUS:84969961419

SN - 1474-7596

VL - 17

JO - Genome Biology

JF - Genome Biology

IS - 1

M1 - 111

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this