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

===== Information =====

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

===== Usage =====

See versions of Trimmomatic which are available:
<code>$ module avail trimmomatic</code>

Load one version into your environment and run it:
<code>$ module load trimmomatic/0.39
$ trimmomatic</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ 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</code>

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

<code>#!/usr/bin/env bash

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