prokka VS funannotate

If you need more accurate ORF(CDS) prediction including functional annotation, I recommend using CLI tools such as prokka, bakta, or DFAST (DFAST is also available in a web version).

reCOGnizer (https://github.com/iquasere/reCOGnizer) can annotate with COGs, and the other databases available at CDD. It obtains all information concerning COGs description and categories, and outputs krona plots and TSV tables in formats easy to analyze. There is also mantis (https://github.com/PedroMTQ/mantis), prokka (https://github.com/tseemann/prokka) and DFAST (https://github.com/nigyta/dfast_core), the latter two work on contigs and the first two are for proteins

I just checked out Prokka, which uses Prodigal to predict genes. They do not seem to have any reservations for viruses. Thus, I recommend using Prokka directly, since that will conveniently add functional annotations.

If you do DNA sequencing and receive the sequencing files as fastq files (normal from sequencing) then spades to assemble the genome, then put it through PROKKA to annotate it. Here's a beginners guide, the most difficult part is downloading the programs onto your laptop.

funannotate is an annotation package designed for fungi, but also works for eukaryotes too.

While we are at it, Jon Palmer, the maintainer/author of Funannotate, is very responsive, super nice, and maintains an extremely complicated code base.