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I will preface this by saying I'm not a microbiologist, so I apologise for any haziness and I'll be happy to expand.

I would like to download the assemblies of different E. coli genomes and group them by their pathotypes (e.g. EPEC, ETEC, EIEC).

I have used enterobase previously to download salmonella genomes broadly by their subspecies, and it does have a set of E. coli genomes. However, they are mainly annotated by their serotype, and not with any broad nomination of pathogenesis. I think I would be able to use the API to grab these serotypes and map them to a type of pathogenicity but that would probably be quite messy.

Does such a database exist? Most I can find are broadly annotated or a are very detailed, but don't allow access to the raw annotation.

Thanks in advance.

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If ENA archive contains such information, then you can access it programatically through the EBI api.

Also you can access the NCBI database programatically through their eutils.

In both cases you can access annotations, though not sure if they contain what you are looking for in all the cases.

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  • $\begingroup$ Thanks for that! I previously tried the NCBI and it turned out to be quite messy. The ENA is a step in the right direction as I can extract the strain information quite nicely. Not quite what I was after but definitely helpful, thanks. $\endgroup$
    – TW93
    Mar 14 '19 at 19:56

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