Finding the MLST sequence type of an isolate

I want to find the MLST sequence type of Vibrio cholerae isolates based on their genome assemblies.

I find I can do it using the 'mlst' tool, described here.

To run it is very simple, e.g.

% mlst --scheme vcholerae assembly.fa

where assembly.fa is my assembly fasta file.

The output looked like this:

assembly.fa     vcholerae       338     adk(14) gyrB(36)        mdh(6)  metE(193)       pntA(11)        purM(1) pyrC(141)

That is, this isolate is ST338 in the Octavia et al MLST scheme for V. cholerae. Easy peasy!

Acknowledgements

Thanks to my colleages Rahma Golicha and Mat Beale for help with this.