There are several ways to create MLST Schemes in the Microbial Genomics Module.
- Create MLST Scheme. Creates an MLST Scheme from sequence lists of reference genomes or assemblies with CDS annotations.
- Download MLST Scheme. Downloads existing MLST schemes from PubMLST.
- Import MLST Scheme. Imports an MLST scheme from a set of fasta files, sequence type info and optional locus metadata.
After a scheme has been obtained the following tools can be used together with the schemes.
- Type With MLST Scheme.
- Add Typing Results to MLST Scheme.
These tools are described in more detail in the following sections.
Finally, in order to be able to use the MLST Schemes outside of the Workbench, a MLST Scheme can be exported by clicking on the Export button and selecting MLST Scheme. To keep the data manageable, this will export the MLST Scheme into a single zip file containing two text files in tsv format, one with the sequence type definitions and sequence type metadata and the second file containing locus metadata, and one fasta file per locus, corresponding to the format used for importing MLST Schemes.