Getting started with the MLST Typing tools
In order to do MLST typing, one must first obtain an MLST Scheme. There are several ways to do this in the CLC Microbial Genomics Module.
- Create MLST Scheme. Creates an MLST Scheme from sequence lists of reference genomes or assemblies with CDS annotations. A template workflow using this tool is also available, see Create MLST Scheme with Sequence Types.
- Download MLST Scheme. Downloads existing MLST Schemes from PubMLST or Institut Pasteur.
- Import MLST Scheme. Imports an MLST Scheme from a set of fasta files, sequence type info, and, optionally, locus metadata.
After a scheme has been obtained, the following tools can be used together with the schemes. 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 CLC Workbench, an MLST Scheme can be exported by clicking on the Export button and selecting MLST Scheme. 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, as well as one fasta file per locus, corresponding to the format used for importing MLST Schemes.