title: Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling.
abstract: 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.
  
  
  
  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.
  
  
  
  Taxonomer enables rapid, accurate, and interactive analyses of metagenomics data on personal computers and mobile devices.
authors.affiliation: Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
authors.forename: Steven
authors.initials: S
authors.lastname: Flygare
authors.affiliation: Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA.
authors.forename: Keith
authors.initials: K
authors.lastname: Simmon
authors.affiliation: Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
authors.forename: Chase
authors.initials: C
authors.lastname: Miller
authors.affiliation: Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Qiao
authors.affiliation: Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
authors.forename: Brett
authors.initials: B
authors.lastname: Kennedy
authors.affiliation: Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
authors.forename: Tonya
authors.initials: T
authors.lastname: Di Sera
authors.affiliation: Department of Pathology, University of Utah, Salt Lake City, UT, USA.
authors.forename: Erin H
authors.initials: EH
authors.lastname: Graf
authors.affiliation: ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA.
authors.forename: Keith D
authors.initials: KD
authors.lastname: Tardif
authors.affiliation: Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Kapusta
authors.affiliation: Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
authors.forename: Shawn
authors.initials: S
authors.lastname: Rynearson
authors.affiliation: Department of Pediatrics, University of Utah, Salt Lake City, UT, USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Stockmann
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: Krista
authors.initials: K
authors.lastname: Queen
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: Suxiang
authors.initials: S
authors.lastname: Tong
authors.affiliation: Department of Pathology, University of Utah, Salt Lake City, UT, USA.|ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA.
authors.forename: Karl V
authors.initials: KV
authors.lastname: Voelkerding
authors.affiliation: Department of Pediatrics, University of Utah, Salt Lake City, UT, USA.
authors.forename: Anne
authors.initials: A
authors.lastname: Blaschke
authors.affiliation: Department of Pediatrics, University of Utah, Salt Lake City, UT, USA.
authors.forename: Carrie L
authors.initials: CL
authors.lastname: Byington
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: Seema
authors.initials: S
authors.lastname: Jain
authors.affiliation: Department of Pediatrics, University of Utah, Salt Lake City, UT, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Pavia
authors.affiliation: Department of Pediatrics, University of Utah, Salt Lake City, UT, USA.
authors.forename: Krow
authors.initials: K
authors.lastname: Ampofo
authors.affiliation: Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA.|USTAR Center for Genetic Discovery, Salt Lake City, UT, USA.
authors.forename: Karen
authors.initials: K
authors.lastname: Eilbeck
authors.affiliation: Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.|USTAR Center for Genetic Discovery, Salt Lake City, UT, USA.
authors.forename: Gabor
authors.initials: G
authors.lastname: Marth
authors.affiliation: Department of Human Genetics, University of Utah, Salt Lake City, UT, USA. myandell@genetics.utah.edu.|USTAR Center for Genetic Discovery, Salt Lake City, UT, USA. myandell@genetics.utah.edu.
authors.forename: Mark
authors.initials: M
authors.lastname: Yandell
authors.affiliation: Department of Pathology, University of Utah, Salt Lake City, UT, USA. robert.schlaberg@path.utah.edu.|ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA. robert.schlaberg@path.utah.edu.
authors.forename: Robert
authors.initials: R
authors.lastname: Schlaberg
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000145:classification / Q000235:genetics; D030561:Databases, Nucleic Acid; D005658:Fungi / Q000145:classification / Q000235:genetics; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions / Q000235:genetics*; D056186:Metagenomics / Q000379:methods*; D012984:Software; D059467:Transcriptome; D014584:User-Computer Interface; D014780:Viruses / Q000145:classification / Q000235:genetics; D064878:Web Browser
keywords: Infectious disease diagnostics; Metagenomics; Microbiome; Pathogen detection