ABSTRACT
Trimming refers to the process of removing low-quality or artefactual sequences or portions of sequences prior to downstream analysis —essentially by surgically eliminating only low quality regions. Quality Trimming applies a filter to segments of reads based on their Phred quality values. Adapter trimming, also known as adapter clipping, removes adapter sequences from NGS reads. Trimmomatic uses the term "technical sequences" to refer to adapter sequences and polymerase chain reaction (PCR) primers, but, for simplicity, in the following we will use the word "adapter". Trimmomatic is a Java executable that can be downloaded from the Usadel lab homepage. Trimming software typically works in stages. With Trimmomatic, the user needs to indicate the stages and the order of the stages. The ILLUMINACLIP argument is as follows: To understand this, it is important to understand how Trimmomatic works. It uses a two step strategy to search for matches between adapters and reads.
