Annotating a genome using a previous annotation file

Question

[arturo.marin]

Hello,

Is there any software that allows annotated a genome using an available annotation file (.gff or .gtf) of the same species as a reference? My idea is to use something like this to make the annotation faster.

Answer 1

[GenoMax]

CrossMap (LINK) or LiftOff (LINK).

[arturo.marin]

Thanks! LiftOff looks nice. I think it will be useful to me. I will have to find a way to parallelize it, maybe with gnu parallel, because I need to analyze thousands of genomes of viruses.

[Juke34]

See table5 of this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450745/ (Whole-Genome Alignment and Comparative Annotation)

LiftOff is not an annotation tool, it will not check start stop codons, or open reading frame. But for viruses it might do the job well anyway. See here https://github.com/agshumate/Liftoff/issues/7

[arturo.marin]

Thanks for your comments here Juke34, and for your comment at Github. I did some test and I was thinking that LiftOff works... but probably it give me some problems because I am interested in study the variations (SNPs and indels) in some ORFs. In addition to this, I opened an issue in the developers web in Github https://github.com/agshumate/Liftoff/issues/70 , because LiftOff don't create a right GFF3. The header of the GFF3 format is missing.