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PSAEC: An Improved Algorithm for Short Read Error Correction Using Partial Suffix Arrays

机译:PSAEC:使用部分后缀数组的短读错误校正的改进算法

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摘要

Sequencing errors in high-throughput sequencing data constitute one of the major problems in analyzing such data. Error correction can reduce the error rate. However, it is a computation and data intensive process for large-scale data. This poses challenges for more efficient and scalable algorithms. In this paper, we propose PSAEC, an improved algorithm for short read error correction using partial suffix arrays in high-throughput sequencing data. Our algorithm optimizes the HiTEC program by replacing full suffix arrays with partial suffix arrays to index reads which is more time and space efficient. Moreover, PSAEC is a scalable parallel algorithm that can works well on multi-core computers using Pthread. Experiments show that our algorithm delivers good, scalable performance.
机译:高通量测序数据中的测序错误是分析此类数据的主要问题之一。纠错可以降低错误率。但是,它是大规模数据的计算和数据密集型过程。这对更有效和可扩展的算法提出了挑战。在本文中,我们提出了PSAEC,一种改进的算法,用于在高通量测序数据中使用部分后缀数组进行短读错误校正。我们的算法通过将完整的后缀数组替换为部分后缀数组来索引读取来优化HiTEC程序,从而节省了时间和空间。而且,PSAEC是一种可扩展的并行算法,可以在使用Pthread的多核计算机上很好地工作。实验表明,我们的算法可提供良好的可扩展性能。

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