[Bioinfo-list] Parameter settings question

Dear all,

With internet connectivity seemingly returning to East Africa, I'll spam the list with some more questions that came up in the CoP meeting. Here's the next.

When running tools like ResFinder and VirulenceFinder, I generally rely on their default cut-off settings (usually: 60% coverage, 90% identity).  Is there an empirical basis for these settings or did someone just pull them out of thin air?

Do the default settings suffice or should we be more judicious? Perhaps use different settings for different species, different AMR genes, when testing on reads vs assemblies?

Marco