BMC Bioinformatics. 2014;15 Suppl 9(Suppl 9):S10. doi: 10.1186/1471-2105-15-S9-S10. Epub 2014 Sep 10.
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.
将配对末端测序的正向和反向读取合并是一项关键任务，通过为它们提供虚拟延长的读取，可以显著提高下游任务（如基因组组装和映射）的性能。然而，由于大多数配对末端测序仪的固有限制，随着读取结束，观察错误碱基的机会迅速增加，这成为准确合并配对末端读取的关键障碍。尽管存在几种复杂的方法来解决这个问题，但它们在合并质量方面的性能往往仍不尽如人意。为了解决这个问题，我们在这里提出了一种用于配对末端读取的上下文感知方案（CASPER）：一种快速而稳健的重叠配对末端读取合并的计算方法。由于特别适合扩增子测序应用，CASPER 经过了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 在准确性和稳健性方面明显优于现有的最先进的配对末端合并工具。CASPER 还利用了配对末端合并任务中的并行性，并通过多线程有效地加速。CASPER 可在 http://best.snu.ac.kr/casper 上免费供学术使用。
