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

Research output: Contribution to journalArticle

80 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 languageEnglish (US)
Article number111
JournalGenome Biology
Volume17
Issue number1
DOIs
StatePublished - May 26 2016

Keywords

  • Infectious disease diagnostics
  • Metagenomics
  • Microbiome
  • Pathogen detection

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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