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)