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I have a large dataset of assemblies of bacterial S. aureus genomes (~1000, same species). I am looking at different tools to estimate the presence of drug-resistance factors such as blaZ or ampC. Though, using three different approaches, I get three different answers. Some of the tools I use are Ariba or Roary after gene annotation with Prokka.

I wonder what are the most reliable tools used in the field to recognize drug-resistance and virulence factors?

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  • $\begingroup$ I think you are in as good a position as anyone to know the answer within MRSA. Ariba has the 'genomics clout', but I'm not sure they are you're standard @Soren. They are genomicists and today is data science, whether impact factor currently reflects that or not. Personally I'd use phylogeny as a starting point, but you know more than I, about ML training, parameterisation and testing. $\endgroup$
    – M__
    Nov 28 '20 at 17:53

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