Viral genome annotation

Question

[h.l.wong]

Hi all,

I have got some viral genomes (using MARVEL) isolated from metagenomics data. I am wondering what programs I can use for functional annotation and taxonomic classifcation for the viral genomes?

I have used PROKKA (specified --kingdom viruses) and eggnogmapper for annotation but I am sure there are programs out there that specifically works on viruses.

Cheers and many thanks

Alan

[Juke34]

There are few tools for virus annotation in that list https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/annotation_tools_genome.md

[h.l.wong]

Thank you for your suggestion!

Answer 1

[Joseph Hughes]

Viruses are super diverse and range hugely in size and the number of genes. Tools that I have found useful for annotation of viruses are RATT, VaPiD and VGas. Each has pros and cons. I would maybe suggest starting with VAPiD but then I am not too sure what your data is like, specifically how novel your virus is.

[h.l.wong]

Thanks! I don't know if the viruses are novel cause I have no idea what programs to classify them. I will try the programs you suggest.