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