# trimmomatic

## Summary

+ **Module Name:** trimmomatic
+ **Support Level:** Primary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [http://www.usadellab.org/cms/?page=trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic)

## Software Description

[From the author\'s web
page:](http://www.usadellab.org/cms/index.php?page=trimmomatic)
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.
## 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
## 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 msismall
	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 /common/software/install/migrated/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