Srst2

Introduction

This python based tool with two main dependencies (samtools and bowtie2) carries out mapping of short reads to detect overall three targets:

1. genes
2. alleles
3. multi-locus sequence types (MLST)

from WGS data (which we can take to be NGS short reads).

A smaller number of loci, i.e. 7, are used to divide the population.

These loci come in the shape of housekeeping genes that all the species and isolates are bound to have.

Glossary

• MLST: MultiLocus Sequence Type