HaploMerger: reconstructing allelic relationships for polymorphic diploid genome assemblies.
HaploMerger: reconstructing allelic relationships for polymorphic diploid genome assemblies.
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HaploMerger：重建多态性二倍体基因组组装的等位基因关系
DOI：
10.1101/gr.133652.111
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发表时间：
2012-08
期刊：
影响因子：
7
通讯作者：
Xu A
中科院分区：
文献类型：
--
作者：
Huang S;Chen Z;Huang G;Yu T;Yang P;Li J;Fu Y;Yuan S;Chen S;Xu A
全基因组鸟枪组装一直是高度多态性基因组的长期问题，下一代测序技术的出现使这个问题比以往任何时候都更具挑战性。在这里，我们提出了一个自动化的管道，HaploMerger，在二倍体组装重建等位基因的关系。HaploMerger将LASTZ-ChainNet比对方法与一种新的基于图的结构相结合，这有助于解开两种单倍型之间的等位基因关系，并指导随后创建参考单倍体组装体。流水线提供灵活的参数和方案，以提高参考程序集的邻接性、连续性和完整性。我们表明，HaploMerger在模拟中产生有效和准确的结果，并且在应用于真实的多态组装时具有优于手动策展的优势（例如，4%-5%杂合性）。我们还利用HaploMerger分析了文昌鱼（Branchiostoma belcheri）的二倍体组装体，并将其与EST序列进行了比较，结果表明，这两种单倍型不仅存在分歧，而且具有高度互补性。综上所述，我们已经证明了HaploMerger是分析和利用多态基因组组装的有效工具。
Whole-genome shotgun assembly has been a long-standing issue for highly polymorphic genomes, and the advent of next-generation sequencing technologies has made the issue more challenging than ever. Here we present an automated pipeline, HaploMerger, for reconstructing allelic relationships in a diploid assembly. HaploMerger combines a LASTZ-ChainNet alignment approach with a novel graph-based structure, which helps to untangle allelic relationships between two haplotypes and guides the subsequent creation of reference haploid assemblies. The pipeline provides flexible parameters and schemes to improve the contiguity, continuity, and completeness of the reference assemblies. We show that HaploMerger produces efficient and accurate results in simulations and has advantages over manual curation when applied to real polymorphic assemblies (e.g., 4%–5% heterozygosity). We also used HaploMerger to analyze the diploid assembly of a single Chinese amphioxus (Branchiostoma belcheri) and compared the resulting haploid assemblies with EST sequences, which revealed that the two haplotypes are not only divergent but also highly complementary to each other. Taken together, we have demonstrated that HaploMerger is an effective tool for analyzing and exploiting polymorphic genome assemblies.
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影响因子：
7
作者：
Vinson, JP;Jaffe, DB;Lander, ES
通讯作者：
Lander, ES
DOI：
10.1093/bioinformatics/btp024
发表时间：
2009-03-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Gouzy J;Carrere S;Schiex T
通讯作者：
Schiex T
影响因子：
14.9
作者：
Zhou L;Pertea M;Delcher AL;Florea L
通讯作者：
Florea L
影响因子：
7
作者：
Barriere, Antoine;Yang, Shiaw-Pyng;Ruvinsky, Ilya
通讯作者：
Ruvinsky, Ilya
DOI：
10.1073/pnas.1932072100
发表时间：
2003-09-30
影响因子：
11.1
作者：
Kent, WJ;Baertsch, R;Haussler, D
通讯作者：
Haussler, D