.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.44.1.
.TH PROKKA "1" "February 2015" "prokka 1.11" "User Commands"
.SH NAME
prokka \- rapid annotation of prokaryotic genomes
.SH DESCRIPTION
.SS "Name:"
.IP
Prokka 1.10 by Torsten Seemann <torsten.seemann@monash.edu>
.SS "Synopsis:"
.IP
rapid bacterial genome annotation
.SS "Usage:"
.IP
prokka [options] <contigs.fasta>
.SS "General:"
.TP
\fB\-\-help\fR
This help
.TP
\fB\-\-version\fR
Print version and exit
.TP
\fB\-\-docs\fR
Show full manual/documentation
.TP
\fB\-\-citation\fR
Print citation for referencing Prokka
.TP
\fB\-\-quiet\fR
No screen output (default OFF)
.SS "Setup:"
.TP
\fB\-\-listdb\fR
List all configured databases
.TP
\fB\-\-setupdb\fR
Index all installed databases
.TP
\fB\-\-cleandb\fR
Remove all database indices
.TP
\fB\-\-depends\fR
List all software dependencies
.SS "Outputs:"
.TP
\fB\-\-outdir\fR [X]
Output folder [auto] (default '')
.TP
\fB\-\-force\fR
Force overwriting existing output folder (default OFF)
.TP
\fB\-\-prefix\fR [X]
Filename output prefix [auto] (default '')
.TP
\fB\-\-addgenes\fR
Add 'gene' features for each 'CDS' feature (default OFF)
.TP
\fB\-\-locustag\fR [X]
Locus tag prefix (default 'PROKKA')
.TP
\fB\-\-increment\fR [N]
Locus tag counter increment (default '1')
.TP
\fB\-\-gffver\fR [N]
GFF version (default '3')
.TP
\fB\-\-compliant\fR
Force Genbank/ENA/DDJB compliance: \fB\-\-addgenes\fR \fB\-\-mincontiglen\fR 200 \fB\-\-centre\fR XXX (default OFF)
.TP
\fB\-\-centre\fR [X]
Sequencing centre ID. (default '')
.SS "Organism details:"
.TP
\fB\-\-genus\fR [X]
Genus name (default 'Genus')
.TP
\fB\-\-species\fR [X]
Species name (default 'species')
.TP
\fB\-\-strain\fR [X]
Strain name (default 'strain')
.TP
\fB\-\-plasmid\fR [X]
Plasmid name or identifier (default '')
.SS "Annotations:"
.TP
\fB\-\-kingdom\fR [X]
Annotation mode:  (default 'Bacteria')
.TP
\fB\-\-gcode\fR [N]
Genetic code / Translation table (set if \fB\-\-kingdom\fR is set) (default '0')
.TP
\fB\-\-gram\fR [X]
Gram: \-/neg +/pos (default '')
.TP
\fB\-\-usegenus\fR
Use genus\-specific BLAST databases (needs \fB\-\-genus\fR) (default OFF)
.TP
\fB\-\-proteins\fR [X]
Fasta file of trusted proteins to first annotate from (default '')
.TP
\fB\-\-metagenome\fR
Improve gene predictions for highly fragmented genomes (default OFF)
.TP
\fB\-\-rawproduct\fR
Do not clean up \fI/product\fP annotation (default OFF)
.SS "Computation:"
.TP
\fB\-\-fast\fR
Fast mode \- skip CDS \fI/product\fP searching (default OFF)
.TP
\fB\-\-cpus\fR [N]
Number of CPUs to use [0=all] (default '8')
.HP
\fB\-\-mincontiglen\fR [N] Minimum contig size [NCBI needs 200] (default '1')
.TP
\fB\-\-evalue\fR [n.n]
Similarity e\-value cut\-off (default '1e\-06')
.TP
\fB\-\-rfam\fR
Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (default '0')
.TP
\fB\-\-norrna\fR
Don't run rRNA search (default OFF)
.TP
\fB\-\-notrna\fR
Don't run tRNA search (default OFF)
.TP
\fB\-\-rnammer\fR
Prefer RNAmmer over Barrnap for rRNA prediction (default OFF)