Scanner: An Efficient and Accurate Trimming Tool for Illumina Next Generation Sequencing Reads

Recent advances in High-Throughput Sequencing (HTS) technology have greatly facilitated the researches in bioinformatics field. With the ultra-high sequencing speed and improved base-calling accuracy, Illumina Genome Analyzer is currently the most widely used platform in the field. To use the raw reads generated from the sequencing machine, the 3’ adapter sequence attached to the real read in the process of ligation needs to be correctly trimmed. This is often done by some inhouse scripts or different packages with various parameters. They either use the Smith-Waterman algorithm or search for an exact match of the 3’ adapter sequence. In this report, I investigated methodologies as well as the strengths and weaknesses of five representative mainstream adapter trimming tools in order to suggest a direction for other researchers. Furthermore, four sets of detailed analysis were performed to evaluate the performances of these tools. I demonstrated that my adapter trimming method is flexible, accurate and efficient for Next Generation Sequencing (NGS) analysis