Getting started with the Large MLST Scheme tools
There are several ways to create Large MLST Schemes in the Microbial Genomics Module.
- Create Large MLST Scheme. Creates a Large MLST Scheme from sequence lists of reference genomes or assemblies with CDS annotations.
- Download Large MLST Scheme. Downloads existing MLST schemes from PubMLST.
- Import Large MLST Scheme. Imports a scheme from a set of text files describing the loci and the sequence types.
After a scheme has been obtained the following tools can be used together with the schemes.
- Type With Large MLST Scheme.
- Add Typing Results to Large MLST Scheme.
These tools are described in more detail in the following sections.
Finally, in order to be able to use the Large MLST Schemes outside of the Workbench, a Large MLST Scheme can be exported by clicking on the Export button and selecting Large MLST Scheme. To keep the data manageable, this will export the Large 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 Large MLST Schemes.