Annotation tools (prokaryotes): prokka vs eggnog

Question

[willnotburn]

Are there any obvious advantages/disadvantages to using one over the other? Both use HMM (I think), both are hierarchical (starting with EggNOG 4.5). Are they simply competitors? Perhaps there is a trade-off between database size (Prokka is smaller) and the quality of curation? I would appreciate any thoughts and/or pointers.

Answer 1

[oschwengers]

Prokka is a more comprehensive annotation pipeline in terms of not only annotating coding genes (CDS) but tRNAs, rRNAs, ncRNAs, CRISPR arrays. In contrast, EggNOG is specifically addressing the annotation of CDS only. As it has this focus and larger databases it is more sensitive in annotating rare CDS. However, by utilizing genus databases Prokka is able to annotate genus specific CDS by potential genus related terms.

So it depends on whether one is interested in CDS only or the entire genome. In that sense it's not quite fair to compare both. There other annotation tools like Prokka, e.g. PGAP, DFAST and Bakta.