Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data
- PMID: 32159761
- DOI: 10.1093/bioinformatics/btaa171
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.
Availability and implementation: Source codes and scripts to reproduce the results descripted in this article are freely available at https://github.com/hellosunking/Ktrim/, distributed under the GPL v3 license.
Contact: sunkun@szbl.ac.cn.
Supplementary information: Supplementary data are available at Bioinformatics online.
© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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