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Trimmomatic

Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.

License

  • Free to use and open source under GNU GPLv3.
  • The license does NOT apply to the sequence of the Illumina sequences contained in the software. THE ILLUMINA sequences (adapters) etc REMAIN COPYRIGHTED and owned by Illumina and are used in Trimmomatic by permission.

Available

  • Roihu-CPU: 0.39, via the bio-apps module.
  • Chipster graphical user interface

Usage

Trimmomatic is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the Trimmomatic module:

module load bio-apps/v202603
module load trimmomatic/0.39

Trimmomatic can be launched with the command:

trimmomatic

If you need to adjust Java settings, such as the maximum heap size, set the _JAVA_OPTIONS environment variable, which the Java runtime picks up automatically:

export _JAVA_OPTIONS="-Xmx8g"

Trimmomatic ships a set of standard Illumina adapter files. The module sets the $TRIMMOMATIC_INSTROOT environment variable, which points to the installation, and the bundled adapter files are located under $TRIMMOMATIC_INSTROOT/share/adapters. Give the path to the adapter file you need in the ILLUMINACLIP step, for example:

ILLUMINACLIP:$TRIMMOMATIC_INSTROOT/share/adapters/TruSeq3-PE.fa:2:30:10

Trimmomatic jobs should be run either in an interactive session or as a batch job.

Example batch job script:

#!/bin/bash
#SBATCH --job-name=trimmomatic
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=00:15:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem=8000

module load bio-apps/v202603
module load trimmomatic/0.39

trimmomatic PE -threads $SLURM_CPUS_PER_TASK -phred33 \
forward.fq.gz reverse.fq.gz \
out_fw_paired.fq.gz out_fw_unpaired.fq.gz out_rev_paired.fq.gz out_rev_unpaired.fq.gz \
ILLUMINACLIP:$TRIMMOMATIC_INSTROOT/share/adapters/TruSeq3-PE.fa:2:30:10 \
LEADING:3 \
TRAILING:3 \
SLIDINGWINDOW:4:15 \
MINLEN:36

The batch job could be launched with command:

sbatch trimmomatic_script

Support

CSC Service Desk

More information