MLST Scheme Tools

The typing and characterization of pathogenic isolates plays an important part in epidemiology and outbreak analysis. MLST (Multilocus Sequence Typing) makes it possible to efficiently type strains against schemes with known isolates.

Whereas classic MLST analysis types isolates against a small set of gene fragments (typical 500bp fragments for a set of seven house-keeping genes), cgMLST (core-genome MLST) and wgMLST (whole-genome MLST) extends the analysis to thousands of loci, usually containing the complete coding gene sequences for the alleles for a given locus.

This section of the manual describes the MLST Scheme tools, which can be used to work with both cgMLST and wgMLST, as well as classic 7-gene schemes. The MLST Scheme typing can be applied either directly to the NGS reads of an isolate, or to an assembly of an isolate.