Hi all! Conceptual question. I know this pipeline is meant for longer reads / contigs, but I'm curious if the following application might work: Is it possible to use funcscan on a whole genome fasta file to identify virulence factors / ARGs that are present in a given genome?

Yes! Basically anything that are not short reads and/or don't have sequence errors in. You can check the tools in the pipelines what they suggest but basically it's xonfigs to full genomes :)