Off topic:What tools are proper to preprocess FASTA coming from Velvet assembler into the Prokka, BG7 and RAST annotators?

Question

[hockeytoronto2018]

What tools are proper to preprocess FASTA coming from Velvet assembler into the Prokka, BG7 and RAST annotators?

I recieve duplication error with Prokka when submitting raw Velvet output. I have tried FASTX-TOOLKIT and no help. Need a Linux software tools to make FASTA digestable to Prokka.