Large 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 a new set of tools, the Large MLST Scheme tools, that can be used to work with both cgMLST and wgMLST, as well as classic 7-gene schemes. The Large MLST Scheme typing can be applied either directly to the NGS reads of an isolate, or to an assembly of an isolate.
Note that the CLC product portfolio provides other tools to work with MLST typing:
- The CLC MLST Module offers functionality for working with classic 7-gene schemes for Sanger sequencing.
- The NGS MLST tools in the CLC Microbial Genomics Module offers functionality for working with classic 7-gene schemes for NGS data, in the form of read mappings.
The NGS MLST and Large MLST tools overlap in functionality. In general, we recommend to use the Large MLST Scheme tools for all NGS applications, as these will eventually replace the NGS MLST functionality.
The Large MLST tools are currently in beta. If you have feedback and feature requests, please get in touch by emailing ts-bioinformatics@qiagen.com.
Subsections
- Getting started with the Large MLST Scheme tools
- Large MLST Scheme Visualization and Management
- Minimum Spanning Trees
- Type With Large MLST Scheme (beta)
- Add Typing Results to Large MLST Scheme (beta)