HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly.
HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly.
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DOI：
10.1093/bioinformatics/btx220
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发表时间：
2017-08-15
期刊：
影响因子：
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通讯作者：
Xu A
中科院分区：
文献类型：
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作者：
Huang S;Kang M;Xu A
杂合二倍体基因组的从头组装是一个困难的问题。高通量短读和长读测序技术的出现为该问题提供了新的挑战和潜在的解决方案。在这里，我们提出了HaploMerger2（HM2），一个自动化的管道，用于从多态性二倍体基因组组装中重建两个单倍体亚组装。它被设计用于处理预先存在的二倍体组装体，这些组装体通常是通过使用从头组装器创建的。HM 2可以处理任何二倍体组装体，但它特别适合于具有高杂合性（≥ 3%）的二倍体组装体，这对于其他工具来说可能是困难的。该流水线还实现了灵活和灵敏的装配错误检测，分层脚手架程序和可靠的间隙关闭方法的单倍体子组件。使用HM 2，我们证明了从真实的高度多态的二倍体组装重建的两个单倍体子组装显示出极大改善的连续性。源代码、可执行文件和测试数据集可在www.example.com上免费获得。 补充数据可在Bioinformatics在线获得。
De novo assembly is a difficult issue for heterozygous diploid genomes. The advent of high-throughput short-read and long-read sequencing technologies provides both new challenges and potential solutions to the issue. Here, we present HaploMerger2 (HM2), an automated pipeline for rebuilding both haploid sub-assemblies from the polymorphic diploid genome assembly. It is designed to work on pre-existing diploid assemblies, which are typically created by using de novo assemblers. HM2 can process any diploid assemblies, but it is especially suitable for diploid assemblies with high heterozygosity (≥3%), which can be difficult for other tools. This pipeline also implements flexible and sensitive assembly error detection, a hierarchical scaffolding procedure and a reliable gap-closing method for haploid sub-assemblies. Using HM2, we demonstrate that two haploid sub-assemblies reconstructed from a real, highly-polymorphic diploid assembly show greatly improved continuity. Source code, executables and the testing dataset are freely available at https://github.com/mapleforest/HaploMerger2/releases/. Supplementary data are available at Bioinformatics online.