Trimmomatic is a tool for various trimming tasks for the Illumina sequencing data. It allows to remove low quality bases from the sequence end and (potentially more importantly) to also remove remaining adapters etc from the reads. One should specify trimming parameters via the command line. It looks a bit awkward at a glance but actually quite easy.
It starts via "java -jar
For example, following code trimming back trailing bases with qualities of under 30 maintaining a read length of at least 50 bp:
java -classpath trimmomatic-0.22.jar org.usadellab.trimmomatic.TrimmomaticSE -phred33 data/s1.fq data/tmp.fq TRAILING:30 MINLEN:50
You can get Trimmomatic files and detailed description here