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B-UMMI / chewBBACA

BSR-Based Allele Calling Algorithm
GNU General Public License v3.0
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Can I get STs with cgMLST? (cgST) #208

Closed juanjo255 closed 2 months ago

juanjo255 commented 2 months ago

Hello @rfm-targa,

Is there a way to get the ST from cgMLST as with MLST? Can you help me understand why its common to get notation from MLST but not from cgMLST?

Thank you for the help,

Juan

ramirma commented 2 months ago

Hi @juanjo255 ,

Thank you for your interest in chewBBACA. The difficulty in obtaining a unique identifier from a genome based MLST method is the potential missing data (i.e. loci which are in the schema but not present in all isolates). If we consider a strict cgMLST, i.e. including loci present in 100% of the strains this could be overcome, but we would probably end up with a much reduced number of loci. If we consider the dataset in question and not the entire species, the cgMLST will be much larger and discriminant but any ST-like identifiers will not be applicable in other contexts.

There are a number of solutions to this problem with LIN codes having gained some acceptance.

Hope to have helped.

Mario

juanjo255 commented 2 months ago

Dr. @ramirma ,

It was very clear.

Thank you very much for the explanation,

Juan