Best state-of-the-art tool for ab initio-based gene prediction / annotation of genome assemblies

Question

[JJ]

Hi all,

I am hoping to get some recommendations for tools to perform ab initio-based gene prediction / annotation of genome assemblies in fungi.

I have come across Genscan, Augustus, GlimmerHMM, GeneID and SNAP. Any recommendation which one is the best and user-friendliest tool?

Thank you!

[Joe]

Augustus and GlimmerHMM are the only 2 I was really aware of. Quite widely used.

You may want to look at the OmicTools website.

Answer 1

[lieven.sterck]

Genscan, Glimmer and SNAP will likely be the most easy to use ones but unfortunately also the least performing.

Augustus will easily outperform the others mentioned, given that it is trained correctly. And that's where the difficult lays: running these software is usually not that difficult, it's applying them correctly to the best of their performance that is the "issue".

One other tool I can recommend is EuGene (simply google "Eugene gene prediction" ), very performant but not so user-friendly though :/