Liftoff

Liftoff is an accurate tool that maps annotations described in General Feature Format (GFF) or General Transfer Format (GTF) between assemblies of the same, or closely related species. Depending on minimap2, liftoff takes two genome assemblies and a reference annotation as inputs and outputs an annotation of the target genome. By design it allows gene sequences to be lifted over between the two genomes despite structural differences.

To Load on Palmetto 2 :

module load biocontainers
module load liftoff

A simple example of liftoff would look roughly like:

liftoff -g GTFFILE.gtf TARGET.fasta REFERENCE.fasta

For additional information please see their github page.

Parallel Capabilities: Single core only.