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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

  • Puhti: 0.39
  • Chipster graphical user interface

Usage

Trimmomatic is included in the biokit module:

module load biokit

It can also be loaded separately:

module load trimmomatic

Trimmomatic can be launched with command:

trimmomatic

If you need to adjust Java settings you can use variable $TMJAR

java <java options> -jar $TMJAR <trimmomatic options>

Included adapter sequences for ILLUMINACLIP can be used by specifying $ADAPTERS, e.g:

ILLUMINACLIP:$ADAPTERS/TruSeq3-PE.fa:2:30:10

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

Example batch job script:

#!/bin/bash
#SBATCH --job-name=trimmomatic
#SBATCH --account=project_12345 # Substitute your project name
#SBATCH --partition=small
#SBATCH --time=00:15:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem=8000

trimmomatic PE -threads $SLURM_CPUS_PER_TASK -phred64 \
forward.fq.gz reverse.fq.gz \
out_fw_paired.fq.gz out_fw_unpaired.fq.gz out_rev_paired.fq.gz out_rev_unpaired.fq.gz \
ILLUMINACLIP:$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

More information