BUSCO for bacterial genome assemblies

[Touraj_Rahimi]

Hi, I’m trying to run BUSCO for some bacterial genome assemblies, in this case prodigal use as default gene prediction, but in galaxy eu, choosing one of three Select a gene predictor options which uses mainly for eukaryotic data has signifcant effect on BUSCO results in bacterial analysis.
Any advice how to use it for bacterial genome?
Best

[jennaj]

Welcome, @Touraj_Rahimi

We have some advice in this topic. Maybe try using MetaEuk?

@mmontonerin

The key problem is that I was not leaving selected MetaEuk as database, as I was working with prokaryotes, but I realized now that the code works with Prodigal in bacterial lineages even if there is no option to select it. I was then selecting Miniprot and I was getting the error. So to solve it it was only a matter of leaving MetaEuk selected for prokaryon genomes.

You could also try Prokka or Funannotate for annotation.

Let’s start there, thanks!