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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

Barrnap

Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal RNA genes in genomes. It supports bacterial, archaeal, mitochondrial and eukaryotic rRNA.

License

Free to use and open source. See the Barrnap license.

Available

  • Roihu: 0.9, via the bio-apps module.

Usage

Barrnap is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the Barrnap module:

module load bio-apps/v202603
module load barrnap/0.9

Barrnap takes a FASTA genome as input and writes rRNA feature predictions in GFF3 format. Select the kingdom with --kingdom (bac, arc, euk or mito) and the number of threads with --threads:

barrnap --kingdom bac --threads 4 genome.fna > rrna.gff

Example batch script

#!/bin/bash
#SBATCH --job-name=barrnap
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=01:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=2G

module load bio-apps/v202603
module load barrnap/0.9

barrnap --kingdom bac --threads $SLURM_CPUS_PER_TASK genome.fna > rrna.gff

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information