How to use Prokka for rapid prokaryotic features annotation
Prokka is one of useful software tools package that use for annotating bacterial, archaeal and viral genomes feature data both automatically and manually.
This tools use Perl for processing data and it only uses core Perl modules. but has quite a few external tool dependencies, some of which we can not bundle due to licence restrictions. Eventually we hope to have a public web-server version, and a version of it in the Galaxy Toolshed.

fast
    supports multi-threading
    hierarchical search databases
simple to use
    no compulsory parameters
    bundled databases
clean
    standards-compliant output files
    pipeline-friendly interface
thorough
    finds tRNA, rRNA, CDS, sig_peptide, tandem repeats, ncRNA
    includes /gene and /EC_number where possible, not just /product
    traceable annotation sources via /inference tags
useful
    produce files close-to-ready for submission to Genbank
    complete log file

It currently takes about 10 minutes on a quad Intel i7 for a typical 4 Mbp genome.

Download Link:
https://bioinformatics.net.au/software.prokka.shtml

Manual Scripts:
https://bioinformatics.net.au/prokka-manual.html