ReMILO: reference assisted misassembly detection algorithm using short and long reads
ReMILO: reference assisted misassembly detection algorithm using short and long reads
复制标题
ReMILO：使用短读和长读的参考辅助错误组装检测算法
DOI：
10.1093/bioinformatics/btx524
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发表时间：
2018-01-01
期刊：
影响因子：
5.8
通讯作者：
Lan, Lingxiao
中科院分区：
文献类型：
--
作者：
Bao, Ergude;Song, Changjin;Lan, Lingxiao
动机
从第二代测序短阅读组装的重叠群可能包含错误组装，从而使下游分析复杂化，甚至导致错误的分析结果。幸运的是，随着越来越多的测序物种可用，使用密切相关物种的参考基因组来检测错误组装成为可能。此外，第三代测序技术的长读数已经得到越来越广泛的应用，并且还可以帮助检测错误组装。
结果
在这里，我们介绍ReMio，这是一种参考辅助错误汇编检测算法，它同时使用短读取和PacBio SMRT长读取。该方法首先将初始短读数与重叠群和参考基因组进行比对，然后构建一种称为红黑多位置de Bruijn图的新数据结构来检测错配。此外，ReMio还将重叠群与长读数对齐，并找出它们与长读数的差异，以检测更多的错配。在我们对人类14号染色体数据短读组件的性能测试中，ReMILO可以检测出41.8-77.9%的广泛错误组装和33.6-54.5%的局部错误组装。在巴氏链霉菌数据的混合短读和长读组件上，ReMILO还可以检测60.6-70.9%的广泛错误组装和28.6-54.0%的局部错误组装。
可用性和实施
根据ARTICAL LICENSE 2.0，可从以下网站免费下载REMLO软件：https://github.com/songc001/remilo.
联系方式
邮箱：baoe@bjtu.edu.cn
补充资料
补充数据可在生物信息学在线上获得。
Motivation
Contigs assembled from the second generation sequencing short reads may contain misassemblies, and thus complicate downstream analysis or even lead to incorrect analysis results. Fortunately, with more and more sequenced species available, it becomes possible to use the reference genome of a closely related species to detect misassemblies. In addition, long reads of the third generation sequencing technology have been more and more widely used, and can also help detect misassemblies.
Results
Here, we introduce ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called red-black multipositional de Bruijn graph to detect misassemblies. In addition, ReMILO also aligns the contigs to long reads and find their differences from the long reads to detect more misassemblies. In our performance test on short read assemblies of human chromosome 14 data, ReMILO can detect 41.8-77.9% extensive misassemblies and 33.6-54.5% local misassemblies. On hybrid short and long read assemblies of S.pastorianus data, ReMILO can also detect 60.6-70.9% extensive misassemblies and 28.6-54.0% local misassemblies.
Availability and implementation
The ReMILO software can be downloaded for free under Artistic License 2.0 from this site: https://github.com/songc001/remilo.
Contact
baoe@bjtu.edu.cn.
Supplementary information
Supplementary data are available at Bioinformatics online.