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srst2 website  

Short Read Sequence Typing for Bacterial Pathogens. This program is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.

Environment Modules

Run module spider srst2 to find out what environment modules are available for this application.

System Variables

  • HPC_SRST2_DIR - installation directory
  • HPC_SRST2_BIN - executable directory


If you publish research that uses srst2 you have to cite it as follows:

Inouye, Michael, et al. "SRST2: Rapid genomic surveillance for public health and hospital microbiology labs." Genome medicine 6.11 (2014): 90.