Trimmomatic

Introduction

Trimmomatic is a flexible read trimming tool for Illumina NGS data

For more information, please check:

BioContainers: https://biocontainers.pro/tools/trimmomatic

Home page: http://www.usadellab.org/cms/index.php?pagetrimmomatic

Versions

• 0.39

Commands

• 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 -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 8
#SBATCH --mem=16G
#SBATCH --job-name=trimmomatic
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load trimmomatic/XXXX ### you can run *module avail trimmomatic* to check all available versions

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