trimmomatic

Module Name

trimmomatic

Last Updated On

08/29/2023

Support Level

Primary Support

Software Access Level

Open Access

Home Page

http://www.usadellab.org/cms/?page=trimmomatic

Software Description

From the author\'s web page: Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.  The selection of trimming steps and their associated parameters are supplied on the command line.

Slurm Example

#!/bin/bash
#SBATCH --job-name="rfm_RunTRIMMOMATICTest_job"
#SBATCH --ntasks=1
#SBATCH --ntasks-per-node=1
#SBATCH --output=rfm_RunTRIMMOMATICTest_job.out
#SBATCH --error=rfm_RunTRIMMOMATICTest_job.err
#SBATCH --time=0:10:0
#SBATCH -p small,large,ram256g,ram1t
module load trimmomatic/0.33
wget https://public.s3.msi.umn.edu/reframe/sw/trimmomatic/Truseq3-SE.fa
wget https://public.s3.msi.umn.edu/reframe/sw/trimmomatic/seq.fq
java -jar /panfs/roc/msisoft/trimmomatic/0.33/trimmomatic.jar SE seq.fq out.fq ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

General Linux

The current trimming steps are: - ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read. SLIDINGWINDOW: Perform a sliding window trimming, cutting once the average quality within the window falls below a threshold. - LEADING: Cut bases off the start of a read, if below a threshold quality - TRAILING: Cut bases off the end of a read, if below a threshold quality - CROP: Cut the read to a specified length - HEADCROP: Cut the specified number of bases from the start of the read - MINLEN: Drop the read if it is below a specified length - TOPHRED33: Convert quality scores to Phred-33 - TOPHRED64: Convert quality scores to Phred-64

It works with FASTQ (using phred + 33 or phred + 64 quality scores, depending on the Illumina pipeline used), either uncompressed or gzipp'ed FASTQ. Use of gzip format is determined based on the .gz extension.

For single-ended data, one input and one output file are specified, plus the processing steps. For paired-end data, two input files are specified, and 4 output files, 2 for the 'paired' output where both reads survived the processing, and 2 for corresponding 'unpaired' output where a read survived, but the partner read did not.

Trimmomatic is a java program accessed via a modules library on the lab cluster.

module load trimmomatic

This loads the default version of Trimmomatic and sets the environment variable TRIMMOMATIC. Then invoke the program:

java -jar $TRIMMOMATIC/trimmomatic.jar

java -Xmx2000M -jar $TRIMMOMATIC/trimmomatic.jar PE R1.fastq R2.fastq R1.PE.fastq R1.SE.fastq R2.PE.fastq R2.SE.fastq ILLUMINACLIP:$TRIMMOMATIC/adapters/NexteraPE-PE.fa:2:30:10:2:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30

The user manual is available at http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf Consider using the risstrim.pl script in the riss_util module, which provides a simplified interface for running Trimmomatic.

module load riss_util
risstrim.pl -h

Default

0.33

Other Modules

0.32, 0.33, 0.39

Default

0.33

Other Modules

0.32, 0.33, 0.39

Default

0.33

Other Modules

0.32, 0.33, 0.39