Trimmomatic performs a variety of trimming tasks for Illumina paired-end and single-end data. It is a pair preprocessing tool optimized for Illumina's next generation sequencing data (NGS).
The software includes several processing steps for trimming and filtering the reading. It uses a pipeline-based architecture that allows individual "steps" (removal of adapters, quality filtering, etc.) to be applied to each read/read pair, in the order specified by the user.