Performs a variety of trimming tasks for Illumina paired-end and single ended data. Trimmomatic is a flexible, pair-aware preprocessing tool, optimized for Illumina next-generation sequencing (NGS) data. The software includes several processing steps for read trimming and filtering. It uses a pipeline-based architecture, allowing individual ‘steps’ (adapter removal, quality filtering, etc.) to be applied to each read/read pair, in the order specified by user.