光滑$q$ -Gram及其在长的、易出错的测序读段之间的重叠检测中的应用
Smooth $q$-Gram, and Its Applications to Detection of Overlaps among Long, Error-Prone Sequencing Reads
摘要：
我们提出了光滑的$q$ -gram，第一个变种的$q$ -gram捕获$q$ -gram对在一个小的编辑距离。我们应用平滑$q$ -gram来检测由单分子实时的测序（SMRT）产生的易出错读段的重叠对的问题，这是SMRT读段的从头片段组装的第一步也是最关键的一步。我们已经实现并测试了我们的算法在一组现实世界的基准。我们的实验结果表明，我们的算法比现有的$q$ -gram为基础的算法的准确性显着的优越性。
英文摘要：
We propose smooth $q$-gram, the first variant of $q$-gram that captures $q$-gram pair within a small edit distance. We apply smooth $q$-gram to the problem of detecting overlapping pairs of error-prone reads produced by single molecule real time sequencing (SMRT), which is the first and most critical step of the de novo fragment assembly of SMRT reads. We have implemented and tested our algorithm on a set of real world benchmarks. Our empirical results demonstrated the significant superiority of our algorithm over the existing $q$-gram based algorithms in accuracy.
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