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?