Ktrim: An extra-fast and accurate adapter- And quality-trimmer for sequencing data

Abstract

Motivation: Next-generation sequencing (NGS) data frequently suffer from poor-quality cycles and adapter contaminations therefore need to be preprocessed before downstream analyses. With the ever-growing throughput and read length of modern sequencers, the preprocessing step turns to be a bottleneck in data analysis due to unmet performance of current tools. Extra-fast and accurate adapter- and quality-trimming tools for sequencing data preprocessing are therefore still of urgent demand. Results: Ktrim was developed in this work. Key features of Ktrim include: built-in support to adapters of common library preparation kits; supports user-supplied, customized adapter sequences; supports both paired-end and single-end data; supports parallelization to accelerate the analysis. Ktrim was ∼2-18 times faster than current tools and also showed high accuracy when applied on the testing datasets. Ktrim could thus serve as a valuable and efficient tool for short-read NGS data preprocessing. Contact: sunkun@szbl.ac.cn