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srst2

Description

srst2 website

srst2 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.

Environment Variables

  • HPC_SRST2_DIR - installation directory
  • HPC_SRST2_BIN - executable directory

Citation

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

Inouye, M., Dashnow, H., Raven, LA. et al. SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Med 6, 90 (2014). https://doi.org/10.1186/s13073-014-0090-6

Categories

sequencing, genomics, biology