Trimmomatic is a package written in JAVA which is designed to perform several important read trimming tasks on Illumina data. It can work with both Illumina paired-end data and single ended data.
Use of Trimmomatic on RCC Resources
To use Trimmomatic on Spear, first load the module:
module load trimmomatic
Then, you can run the package with the following syntax:
java -jar $trimmomatic [input/output parameters]
The available input/output parameters are discussed in the online documentation for Trimmomatic.