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.

You can also use a zipped file, e.g. assembly.fa.gz. 

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!

 

If your genome has novel alleles, there is no ST given, and the allele number given is negative, e.g.

assembly.fa  vcholerae       -       adk(2)  gyrB(62)        mdh(7)  metE(413)       pntA(~84)       purM(60)        pyrC(145)

You can get the mlst software to print out the sequence of the novel alleles by typing:

 % mlst --scheme vcholerae assembly.fa -novel novel_alleles.fa

where novel_alleles.fa is the file where you want the sequence(s) of novel alleles to be saved. 

 

 You can see more details on the mlst tool website.

Acknowledgements

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