Hello mag users ! What tool do you recommand for functional annotation of the MAGs retrieved with the pipeline. I was looking for something running Kofam, Pfam and Cazymes datasets like DRAM (having trouble running it right now)

Depends on exactly what you're looking for, but #C02K5GX2W93 will be relatively soon supporting CAZyme screening

For now, I'm just looking to have a working pipeline from raw reads to functionally annotated MAGs

@Evangelos Karatzas does #C084HP11VPF or something help with this somehow?

on the amino acid sequence level, yes. you'll have to pass the predicted proteins in a samplesheet and then run #C084HP11VPF. If you have multiple species from mag, you could first pass all the proteins through #C07URFZF074 first to scale down, and then use the produced family representative sequences only as input in #C084HP11VPF

I guess you could take the `faa`from prokka for it?