Supported Applications

Trimmomatic

Description

a flexible read trimming tool for Illumina NGS data.
Usage
To list all executables provided by Trimmomatic, run: $ biogrids-list trimmomatic
Usage Notes

The alias trimmomatic may be used in place of the full command java -jar trimmomatic-0.35.jar

For example, to run this command within the BioGrids environment:

java -jar trimmomatic-0.35.jar SE -phred33 input.fq.gz output.fq.gz ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

use the alias:

trimmomatic SE -phred33 input.fq.gz output.fq.gz ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

Use of the alias ensures the proper java version is called.
Installation
Use the following command to install this title with the CLI client: $ biogrids-cli install trimmomatic Available operating systems: Linux 64, OS X INTEL
Primary Citation*

A. M. Bolger, M. Lohse, and B. Usadel. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15): 2114-2120.
- *Full citation information available through