What are the offline tools available for the Eukaryotic genome annotation (including fungi, algae, animal and plant ) ?

Question

[Kumar]

I have assembled a genome of a fungi. Now I need to annotate the genome. Please let me know what are the offline tools are available to do the same?

Thank you in advance.

[Mensur Dlakic]

Many people use Latin plurals such as fungi, bacteria or alumni even when they are talking about singular entities. Some know better but do it out of laziness, while others simply don't know. If you are in the latter category: a genome of a fungus.

Answer 1

[shelkmike]

Several years ago I read a couple of articles about eukaryotic genome annotation tools. The best tool (at least, back then) was probably BRAKER (https://github.com/Gaius-Augustus/BRAKER). Since then I annotated many plant genomes with it and was content with results. Details on how I run BRAKER and postprocess its results are described, for example, in https://www.biorxiv.org/content/10.1101/2023.02.14.528432v3 .