Title

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

Authors

Xiang Zhou, Washington University in St Louis

Document Type

Technical Report

Department

Computer Science and Engineering

Publication Date

2013

Filename

WUCSE-2013-1.pdf

DOI:

10.7936/K7BG2M7H

Technical Report Number

WUCSE-2013-1

Abstract

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.

Comments

Permanent URL: http://dx.doi.org/10.7936/K7BG2M7H

Recommended Citation

Zhou, Xiang, "Scanner: An Efficient and Accurate Trimming Tool for Illumina Next Generation Sequencing Reads" Report Number: WUCSE-2013-1 (2013). All Computer Science and Engineering Research.
https://openscholarship.wustl.edu/cse_research/96