---
name: "prokka"
section: "1"
platform: "linux"
package: "prokka"
version: "1.14.6+dfsg-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/prokka"
---

# prokka(1)

rapid annotation of prokaryotic genomes

## 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)