tools for MLST analysis

Question

[hafiz.talhamalik]

is there any tool to perform MLST analysis of bacterial whole genome samples/assembly ??

[Garan]

Any particular bacterial species? Public Health England has one for Salmonella, although it's abit old now:

https://github.com/phe-bioinformatics/MOST

[Joe]

My colleagues at warwick have largely superceded it with Enterobase:

https://enterobase.warwick.ac.uk/

(If you bacteria is one of those in the DB).

Answer 1

[Joe]

Yes, loads. Have you googled?

[hafiz.talhamalik]

yes I did. the ones I found out were paid

[Joe]

I find that highly unlikely:

• https://pubmlst.org/software/database/bigsdb/
• http://sanger-pathogens.github.io/mlst_check/
• https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12170

As I say, there are lots.