Trimmomatic

Introduction

Trimmomatic is a flexible read trimming tool for Illumina NGS data.

For more information, please check its website: https://biocontainers.pro/tools/trimmomatic and its home page: http://www.usadellab.org/cms/index.php?page=trimmomatic.

Versions

0.39

Commands

trimmomatic

Module

You can load the modules by:

module load biocontainers
module load trimmomatic

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 Trimmomatic on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=trimmomatic
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers trimmomatic

trimmomatic PE -threads 8 \
    input_forward.fq.gz input_reverse.fq.gz \
    output_forward_paired.fq.gz output_forward_unpaired.fq.gz \
    output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz \
    ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:36