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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.

GetOrganelle

GetOrganelle is a toolkit for assembling organelle genomes (chloroplast, mitochondrial and nuclear ribosomal DNA) from whole-genome sequencing data.

License

Free to use and open source under GNU GPLv3.

Available

  • Roihu: 1.7.7.1, via the bio-apps module.

Usage

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

module load bio-apps/v202603
module load getorganelle/1.7.7.1

Databases

GetOrganelle needs seed and label databases for the organelle types you want to assemble. Configure them with get_organelle_config.py. By default these are stored under ~/.GetOrganelle; you can choose another location by setting the GETORG_PATH environment variable (for example to a directory in your project's /scratch).

export GETORG_PATH=/scratch/<project>/getorganelle
get_organelle_config.py --add embplant_pt,embplant_mt

Running GetOrganelle

For example, to assemble a plant plastome from paired-end reads:

#!/bin/bash
#SBATCH --job-name=getorganelle
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=12:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=4G

module load bio-apps/v202603
module load getorganelle/1.7.7.1

export GETORG_PATH=/scratch/<project>/getorganelle

get_organelle_from_reads.py -1 read1.fq.gz -2 read2.fq.gz \
    -o plastome_out -F embplant_pt -t $SLURM_CPUS_PER_TASK

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