Trimmomatic

Trimmomatic has been centrally installed on the cluster using a wrapper script, this slightly changes how it operates. loading the module loads all of the dependencies

module load trimmomatic/0.39

Usage Example

This is a basic template of how to run reads first in a bash script on KewHPC

#!/bin/bash
#SBATCH -J trimmomatic_example
#SBATCH -e /data/users_area/myuser/errout/trimmomaticr_%A.err
#SBATCH -o /data/users_area/myuser/errout/trimmomatic_%A.out
#SBATCH -c 8 
#SBATCH -p all

module load trimmomatic/0.39

trimmomatic PE -threads 8 -phred64 -basein infile1 infile2 -baseout outfile