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CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing

Cited 17 time in Web of Science Cited 18 time in Scopus
Authors
Kwon, Sunyoung; Lee, Byunghan; Yoon, Sungroh
Issue Date
2014-09-10
Publisher
BioMed Central
Citation
BMC Bioinformatics, 15(Suppl 9):S10
Description
This is an Open Access article distributed under the terms of the Creative Commons
Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction
in any medium, provided the original work is properly cited.
Abstract
Abstract
Merging the forward and reverse reads from paired-end sequencing is a critical task that can significantly improve the performance of downstream tasks, such as genome assembly and mapping, by providing them with virtually elongated reads. However, due to the inherent limitations of most paired-end sequencers, the chance of observing erroneous bases grows rapidly as the end of a read is approached, which becomes a critical hurdle for accurately merging paired-end reads. Although there exist several sophisticated approaches to this problem, their performance in terms of quality of merging often remains unsatisfactory. To address this issue, here we present a c ontext-a ware scheme for p aired-e nd r eads (CASPER): a computational method to rapidly and robustly merge overlapping paired-end reads. Being particularly well suited to amplicon sequencing applications, CASPER is thoroughly tested with both simulated and real high-throughput amplicon sequencing data. According to our experimental results, CASPER significantly outperforms existing state-of-the art paired-end merging tools in terms of accuracy and robustness. CASPER also exploits the parallelism in the task of paired-end merging and effectively speeds up by multithreading. CASPER is freely available for academic use at http://best.snu.ac.kr/casper.
Language
English
URI
http://hdl.handle.net/10371/100435
DOI
https://doi.org/10.1186/1471-2105-15-S9-S10
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College of Engineering/Engineering Practice School (공과대학/대학원)Dept. of Electrical and Computer Engineering (전기·정보공학부)Journal Papers (저널논문_전기·정보공학부)
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