NAME

       prokka - rapid annotation of prokaryotic genomes

DESCRIPTION

   Name:
              Prokka 1.10 by Torsten Seemann <torsten.seemann@monash.edu>

   Synopsis:
              rapid bacterial genome annotation

   Usage:
              prokka [options] <contigs.fasta>

   General:
       --help This help

       --version
              Print version and exit

       --docs Show full manual/documentation

       --citation
              Print citation for referencing Prokka

       --quiet
              No screen output (default OFF)

   Setup:
       --listdb
              List all configured databases

       --setupdb
              Index all installed databases

       --cleandb
              Remove all database indices

       --depends
              List all software dependencies

   Outputs:
       --outdir [X]
              Output folder [auto] (default '')

       --force
              Force overwriting existing output folder (default OFF)

       --prefix [X]
              Filename output prefix [auto] (default '')

       --addgenes
              Add 'gene' features for each 'CDS' feature (default OFF)

       --locustag [X]
              Locus tag prefix (default 'PROKKA')

       --increment [N]
              Locus tag counter increment (default '1')

       --gffver [N]
              GFF version (default '3')

       --compliant
              Force  Genbank/ENA/DDJB  compliance:  --addgenes  --mincontiglen  200  --centre XXX
              (default OFF)

       --centre [X]
              Sequencing centre ID. (default '')

   Organism details:
       --genus [X]
              Genus name (default 'Genus')

       --species [X]
              Species name (default 'species')

       --strain [X]
              Strain name (default 'strain')

       --plasmid [X]
              Plasmid name or identifier (default '')

   Annotations:
       --kingdom [X]
              Annotation mode:  (default 'Bacteria')

       --gcode [N]
              Genetic code / Translation table (set if --kingdom is set) (default '0')

       --gram [X]
              Gram: -/neg +/pos (default '')

       --usegenus
              Use genus-specific BLAST databases (needs --genus) (default OFF)

       --proteins [X]
              Fasta file of trusted proteins to first annotate from (default '')

       --metagenome
              Improve gene predictions for highly fragmented genomes (default OFF)

       --rawproduct
              Do not clean up /product annotation (default OFF)

   Computation:
       --fast Fast mode - skip CDS /product searching (default OFF)

       --cpus [N]
              Number of CPUs to use [0=all] (default '8')

       --mincontiglen [N] Minimum contig size [NCBI needs 200] (default '1')

       --evalue [n.n]
              Similarity e-value cut-off (default '1e-06')

       --rfam Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (default '0')

       --norrna
              Don't run rRNA search (default OFF)

       --notrna
              Don't run tRNA search (default OFF)

       --rnammer
              Prefer RNAmmer over Barrnap for rRNA prediction (default OFF)