Run Prokka with reference annotation

[lisa-mariebarf]

Add the possibility to run Prokka with good quality reference genomes to ensure gene naming is consistent.
prokka --proteins *.gbk

[klamkiew]

but is *.gbk correct? To me, it looks like prokka only expects one input file with this option and then uses this for the initial annotation? The wildcard looks like several gbk are valid?

[lisa-mariebarf]

You are right, only one fasta file is expected as the argument for the --proteins option
--proteins [X] Fasta file of trusted proteins to first annotate from (default '')

[hoelzer]

We (Charlotte) just recently run this and I think she provided a gbk file from NCBI.

[hoelzer]

 prokka --proteins <ref.gb> --outdir <folder> --prefix <prefix> <.fasta file>