REXTAL: Regional Extension of Assemblies Using Linked-Reads.

Bioinformatics research and applications : 14th International Symposium, ISBRA 2018, Beijing, China, June 8-11, 2018, Proceedings. ISBRA (Conference) (14th : 2018 : Beijing, China) Pub Date : 2018-06-01 Epub Date: 2018-07-13 DOI:10.1007/978-3-319-94968-0_6

Tunazzina Islam, Desh Ranjan, Eleanor Young, Ming Xiao, Mohammad Zubair, Harold Riethman

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引用次数: 2

Abstract

It is currently impossible to get complete de-novo assembly of segmentally duplicated genome regions using genome-wide short-read datasets. Here, we devise a new computational method called Regional Extension of Assemblies Using Linked-Reads (REXTAL) for improved region-specific assembly of segmental duplication-containing DNA, leveraging genomic short-read datasets generated from large DNA molecules partitioned and barcoded using the "Gel Bead in Emulsion" (GEM) microfluidic method (Zheng et al., 2016). We show that using REXTAL, it is possible to extend assembly of single-copy diploid DNA into adjacent, otherwise inaccessible subtelomere segmental duplication regions and other subtelomeric gap regions. Moreover, REXTAL is computationally more efficient for the directed assembly of such regions from multiple genomes (e.g., for the comparison of structural variation) than genome-wide assembly approaches.

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REXTAL:使用链接读取的程序集的区域扩展。

目前不可能使用全基因组短读数据集获得完整的片段重复基因组区域的从头组装。在这里，我们设计了一种新的计算方法，称为使用链接阅读的组装区域扩展(REXTAL)，用于改进含有重复片段的DNA的区域特异性组装，利用使用“凝胶珠在乳液”(GEM)微流控方法分割和条形码的大DNA分子生成的基因组短读数据集(Zheng等，2016)。我们表明，使用REXTAL，可以将单拷贝二倍体DNA的组装扩展到相邻的，否则无法进入的亚端粒片段重复区域和其他亚端粒间隙区域。此外，对于来自多个基因组的这些区域的定向组装(例如，用于结构变异的比较)，REXTAL在计算上比全基因组组装方法更有效。

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Bioinformatics research and applications : 14th International Symposium, ISBRA 2018, Beijing, China, June 8-11, 2018, Proceedings. ISBRA (Conference) (14th : 2018 : Beijing, China)

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