cgMLST version schemes; API download vs web based

Hello,

We are having some issues understanding the versioning of the Salmonella cgMLST database(s)…

We used the API example provided in the help documentation to retrieve the Salmonella cgMLST database at the following address:

http://enterobase.warwick.ac.uk/api/v2.0/senterica/cgMLST/loci?limit=4000

We noticed that this scheme looks to be in concordance with the Salmonella.cgMLSTv4 scheme available here:

http://enterobase.warwick.ac.uk/schemes/Salmonella.cgMLSTv4

That said, it looks like when sequence typing through the web interface, despite choosing “cgMLST v2”, it appears to be running with wgMLST_cgMLSTv1 (http://enterobase.warwick.ac.uk/schemes/SALwgMLST.cgMLSTv1/) as the scheme. We have not figured out how to retrieve this yet through the API.

In developing our own in-house cgMLST typing scripts, we noticed large discrepancies between the web-interface results and our own (which uses the Salmonella.cgMLSTv4 scheme). We assume this is because we are using different versions of the schemes.

Some questions:

1) In order to best perform cgMLST typing in-house (with a custom script), what scheme should we be using?

2) In order to stay up to date with the ‘best’ cgMLST database, what should we be downloading?

Thanks for your help.

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