SRST2: Rapid genomic surveillance for public health and hospital microbiology labs.
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ABSTRACT:
SUBMITTER: Inouye M
PROVIDER: S-EPMC4237778 | biostudies-literature | 2014
REPOSITORIES: biostudies-literature
Publications
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs.
Inouye Michael M Dashnow Harriet H Raven Lesley-Ann LA Schultz Mark B MB Pope Bernard J BJ Tomita Takehiro T Zobel Justin J Holt Kathryn E KE
Genome medicine 20141120 11
Rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet routine use of whole genome sequencing (WGS) for these purposes poses significant challenges. Here we present SRST2, a read mapping-based tool for fast and accurate detection of genes, alleles and multi-locus sequence types (MLST) from WGS data. Using >900 genomes from common pathogens, we show SRST2 is highly accurate and outperforms assembly-based methods in terms o ...[more]
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