LoRDEC: a tool for correcting errors in long sequencing reads 纠正长序列读取错误的工具

LoRDEC: a tool for correcting errors in long sequencing reads

Eric Rivals

21st August 2015

Abstract for keynote presentation at “German Conference in Bioinformatics”, Dortmund, Germany

Address: Laboratoire d’Informatique de Microélectronique et de Robotique de Montpellier (LIRMM) and Institute of Computational Biology (IBC)

CNRS and Université de Montpellier, France – http://www.lirmm.fr/˜rivals/

High-throughput DNA/RNA sequencing is a routine experiment in molecular biology and life sciences in general. For instance, it is increasingly used in the hospital as a key procedure of personalized medicine. Compared to the second generation, third generation sequencing technologies produce longer reads with comparatively lower throughput and higher error rate. Those errors include substitutions, indels, and they hinder or at least complicate downstream analysis like mapping or de novo assembly. However, these long read data are often used in conjunction with short reads of the 2nd generation.

I will present a hybrid strategy for correcting the long reads using the short reads that we introduced last year. Unlike existing error correction tools, ours, called LoRDEC, avoids aligning short reads on long reads, which is computationally intensive. Instead, it takes advantage of a succinct graph to represent the short reads, and compares long reads to paths in the graph. Experiments show that LoRDEC outperforms existing methods in running time and memory while achieving a comparable correction performance. It can correct both Pacific Biosciences and MinION reads from Oxford Nanopore.

LoRDEC is available at http://atgc.lirmm.fr/lordec; joint work with L. Salmela and A. Makrini

高通量DNA/RNA测序是分子生物学和生命科学的常规实验。

例如，它越来越多地作为个性化医疗的关键程序在医院中使用。

与第二代测序技术相比，第三代测序技术的读取时间更长，吞吐量更低，出错率更高。

这些错误包括替换、插入，它们妨碍或至少使下游分析(如映射或从头组装)复杂化。然而，这些长读数据通常与第二代的短读一起使用。我将提出一种混合策略，使用我们去年引入的短读来纠正长读。

与现有的纠错工具不同，我们的LoRDEC避免了长读和短读之间的对齐，这需要大量的计算。相反，它利用简洁的图来表示短读，并将长读与图中的路径进行比较。实验表明，LoRDEC在运行时间和内存方面优于现有的方法，同时获得了相当的校正性能。它可以纠正太平洋生物科学和MinION读取牛津纳米孔。

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LoRDEC: a tool for correcting errors in long sequencing reads 纠正长序列读取错误的工具

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