Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling. - PubMed - NCBI
Genome Biol. 2016 May 26;17(1):111. doi: 10.1186/s13059-016-0969-1.
Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling.
Flygare S1,
Simmon K2,
Miller C1,
Qiao Y1,
Kennedy B1,
Di Sera T1,
Graf EH3,
Tardif KD4,
Kapusta A1,
Rynearson S1,
Stockmann C5,
Queen K6,
Tong S6,
Voelkerding KV3,4,
Blaschke A5,
Byington CL5,
Jain S6,
Pavia A5,
Ampofo K5,
Eilbeck K2,7,
Marth G1,7,
Yandell M8,9,
Schlaberg R10,11.
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
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