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trimmomatic-software

Trimmomatic

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

Information

Usage

See versions of Trimmomatic which are available:

$ module avail trimmomatic

Load one version into your environment and run it:

$ module load trimmomatic/0.38
$ trimmomatic

Installation

Notes from the sysadmin during installation:

$ cd /tmp
$ wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip
$ unzip Trimmomatic-0.38.zip
$ sudo mkdir -p /export/apps/trimmomatic/0.38
$ sudo cp -r Trimmomatic-0.38/* /export/apps/trimmomatic/0.38

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-0.38.jar $*
trimmomatic-software.txt · Last modified: 2018/06/02 02:03 by aorth