CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing.
CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing.
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DOI：
10.1186/1471-2105-15-s9-s10
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发表时间：
2014
影响因子：
3
通讯作者：
Yoon S
中科院分区：
文献类型：
--
作者：
Kwon S;Lee B;Yoon S
合并双端测序的正向和反向读取是一项关键任务，可以通过为下游任务（例如基因组组装和作图）提供几乎拉长的读取来显着提高其性能。然而，由于大多数双端测序仪的固有局限性，随着读段接近末尾，观察到错误碱基的机会迅速增加，这成为准确合并双端读段的关键障碍。尽管存在多种解决此问题的复杂方法，但它们在合并质量方面的性能通常仍不能令人满意。为了解决这个问题，我们在这里提出了一种上下文感知的双端读取方案（CASPER）：一种快速、稳健地合并重叠双端读取的计算方法。 CASPER 特别适合扩增子测序应用，并经过模拟和真实高通量扩增子测序数据的全面测试。根据我们的实验结果，CASPER 在准确性和鲁棒性方面显着优于现有最先进的双端合并工具。 CASPER 还利用了双端合并任务中的并行性，并通过多线程有效地加速。 CASPER 可免费用于学术用途，网址为：http://best.snu.ac.kr/casper。
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 context-aware scheme for paired-end reads (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.