getorganelle
Link to section 'Introduction' of 'getorganelle' Introduction
GetOrganelle is a fast and versatile toolkit for accurate de novo assembly of organelle genomes.
For more information, please check its website: https://biocontainers.pro/tools/getorganelle and its home page on https://github.com/Kinggerm/GetOrganelle.
Link to section 'Versions' of 'getorganelle' Versions
-
1.7.7.0
Link to section 'Commands' of 'getorganelle' Commands
- get_organelle_config.py
- get_organelle_from_assembly.py
- get_organelle_from_reads.py
- slim_graph.py
- summary_get_organelle_output.py
Link to section 'Module' of 'getorganelle' Module
You can load the modules by:
module load biocontainers
module load getorganelle
Link to section 'Example job' of 'getorganelle' Example job
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
get_organelle_config.py --add embplant_pt,embplant_mt
get_organelle_from_reads.py -1 Arabidopsis_simulated.1.fq.gz \
-2 Arabidopsis_simulated.2.fq.gz -t 1 -o Arabidopsis_simulated.plastome \
-F embplant_pt -R 10