LoRDEC: accurate and efficient long read error correction
LoRDEC: accurate and efficient long read error correction
复制标题
DOI：
10.1093/bioinformatics/btu538
复制
发表时间：
2014-12-15
期刊：
影响因子：
5.8
通讯作者：
Rivals, Eric
中科院分区：
文献类型：
--
作者：
Salmela, Leena;Rivals, Eric
动机：PacBio单分子实时测序是第三代测序技术，产生长读段，具有相对较低的通量和较高的错误率。错误包括大量的插入缺失和复杂的下游分析，如作图或从头组装。已经提出了利用第二代短读段的高准确性的混合策略来校正长读段。将短读段映射到长读段上可以提供足够的覆盖率，消除高达99%的错误，但代价是运行时间过长，占用大量磁盘和内存空间。我们提出了LoRDEC，一种混合纠错方法，它构建了一个简洁的de Bruijn图来表示短读段，并通过遍历图中所选的路径来为长读段中的每个错误区域寻找纠正序列。相比之下，LoRDEC至少快6倍，所需的内存或磁盘空间比现有工具少93%，同时达到相当的准确性。
Motivation: PacBio single molecule real-time sequencing is a third-generation sequencing technique producing long reads, with comparatively lower throughput and higher error rate. Errors include numerous indels and complicate downstream analysis like mapping or de novo assembly. A hybrid strategy that takes advantage of the high accuracy of second-generation short reads has been proposed for correcting long reads. Mapping of short reads on long reads provides sufficient coverage to eliminate up to 99% of errors, however, at the expense of prohibitive running times and considerable amounts of disk and memory space.Results: We present LoRDEC, a hybrid error correction method that builds a succinct de Bruijn graph representing the short reads, and seeks a corrective sequence for each erroneous region in the long reads by traversing chosen paths in the graph. In comparison, LoRDEC is at least six times faster and requires at least 93% less memory or disk space than available tools, while achieving comparable accuracy.