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hoelzer-lab / ribap

A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
GNU General Public License v3.0
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Run Prokka with reference annotation #34

Closed lisa-mariebarf closed 2 years ago

lisa-mariebarf commented 2 years ago

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

klamkiew commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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

hoelzer commented 2 years ago 
 prokka --proteins <ref.gb> --outdir <folder> --prefix <prefix> <.fasta file>