Trimmomatic is a flexible read trimming tool for Illumina NGS data.

• Version: 0.39
• Added: September, 2015
• Updated: September, 2021
• Link: https://github.com/usadellab/Trimmomatic

See versions of Trimmomatic which are available:

$ module avail trimmomatic

Load one version into your environment and run it:

$ module load trimmomatic/0.39
$ trimmomatic

Notes from the sysadmin during installation:

$ cd /tmp
$ wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip
$ unzip Trimmomatic-0.39.zip
$ sudo mkdir -p /export/apps/trimmomatic/0.39
$ sudo cp -r Trimmomatic-0.39/* /export/apps/trimmomatic/0.39

Trimmomatic is distributed as a jar file and is not easy for users to run. I created a wrapper shell script named trimmomatic:

#!/usr/bin/env bash

readonly PREFIX=$(dirname $0)
java -jar $PREFIX/trimmomatic-0.39.jar $*