SRST2 - 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.

Manuscript: Inouye et al, Genome Medicine, 2014

Story behind the paper: blog posts from the Holt lab and BioMed Central

Using SRST2

Installation and documentation
Example/tutorial
Bugs and feature requests? Please use github issue tracking
Want to hear about updates? Subscribe to the SRST2 google group

Dependencies (latest release SRST2 v0.1.8 - March 15, 2016):

More from the Holt lab and the Inouye lab.

How SRST2 works