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

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


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Bacteria / classification
  • Bacteria / genetics
  • Databases, Nucleic Acid
  • Fungi / classification
  • Fungi / genetics
  • Gene Expression Profiling*
  • High-Throughput Nucleotide Sequencing
  • Host-Pathogen Interactions / genetics*
  • Metagenomics / methods*
  • Software*
  • Transcriptome*
  • User-Computer Interface
  • Viruses / classification
  • Viruses / genetics
  • Web Browser