Getorganelle

Introduction

GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/getorganelle
Home page: https://github.com/Kinggerm/GetOrganelle

Versions

  • 1.7.7.0

Commands

  • get_organelle_config.py

  • get_organelle_from_assembly.py

  • get_organelle_from_reads.py

  • slim_graph.py

  • summary_get_organelle_output.py

Module

You can load the modules by:

module load biocontainers
module load getorganelle

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run getorganelle on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=getorganelle
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers getorganelle