What software is a good standalone alternative to the Prokka genome annotation software?

Question

[bioinformatics_bel]

What software is a good standalone alternative to the Prokka genome annotation software?

Answer 1

[niklas]

As of my writing Prokka's last release was v1.14.5 on Nov. 11, 2019 [1], nearly 5 years ago.

I've heard that Bakta [2] is supposed to be better. It seems also to be actively developed. However, it only (?) works on bacteria.

[1] https://github.com/tseemann/prokka

[2] https://github.com/oschwengers/bakta

[GenoMax]

If you are looking for tools for Eukaryotic genomes then check --> How to annotate eukaryotic genome

Answer 2

[h.mon]

I don't think there are standalone alternatives to Prokka, as Prokka (and alternatives to it) are complete pipelines for bacterial annotation and preparation for submission to NCBI.

For the end user, annotation servers may be considered as "standalone" solutions. The RAST server is quite good, and if you submit to NCBI, you can annotate with PGAP.