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Deprecated: Implicit conversion from float 265.2 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Genome+Biol 2016 ; 17 (ä): ä Nephropedia Template TP
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Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling #MMPMID27224977
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
Genome Biol 2016[]; 17 (ä): ä PMID27224977show ga
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. Electronic supplementary material: The online version of this article (doi:10.1186/s13059-016-0969-1) contains supplementary material, which is available to authorized users.