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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