Prokka

Overview

Prokka is a software for rapid prokaryotic annotation of baterical, archael, and viral genomes. The output .gff files can be used by Roary.

Availability

Cluster	Module/Version
BOSE	prokka/1.14.5
BGSC	Not Available

Note: You can simply use module load prokka to activate the most recently installed version of this software.

Arguments / Options

This is a list of arguments for the prokka command that we wanted to highlight.

Option	Description
--help	help guide listing all available arguments
--outdir	output directory
--force	overwrite existing output
--compliant	force genebank compliance

Sample Slurm Script

submit.sh

#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]

# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32     # How many CPU cores do you want to request
#SBATCH --nodes=1                # How many nodes do you want to request

# -- SCRIPT COMMANDS -- #

# Load the needed modules
module load prokka    # Load Prokka
prokka input.fa

Real Example

Has your research group used Prokka in a project? Contact the HPC Team and we'd be glad to feature your work.

Citation

Please include the following citation in your papers to support continued development of Prokka. Further details are available when you use the command prokka --citation.

Seemann T. Prokka: rapid prokaryotic genome annotation Bioinformatics 2014 Jul 15;30(14):2068-9. PMID:24642063