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Trimmomatic is a tool for trimming Illumina FASTQ data and removing adapters.  When data is sequenced on Illumina, adapters are added for the fragments to attach to the beads.  If these adapters are not removed they can result in false assembly or other issues.  Additionally, the quality of the sequences varies across the length of the read, and poorer quality regions can be trimmed using Trimmomatic.  Running Trimmomatic is a good first step in quality filtering your Illumina data. 

To run it on the HPCC (for example trimming paired-end reads):

java -jar /opt/software/Trimmomatic/0.36-Java-1.8.0_92/trimmomatic-0.36.jar PE [-threads <threads] [-phred33 | -phred64] [-trimlog <logFile>] <input 1> <input 2> <paired output 1> <unpaired output 1> <paired output 2> <unpaired output 2> <step 1> ...

Read the manual for how to use it. Note that the adapter sequence files are in /opt/software/Trimmomatic/0.36-Java-1.8.0_92/adapters/. If you couldn't find the adapters you need in that directory, you will need to obtain them from elsewhere (for example asking the person who ran the library prep for you).