Identifying and removing haplotypic duplication in primary genome assemblies
Identifying and removing haplotypic duplication in primary genome assemblies
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DOI：
10.1093/bioinformatics/btaa025
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发表时间：
2020-05-01
期刊：
影响因子：
5.8
通讯作者：
Durbin, Richard
中科院分区：
文献类型：
--
作者：
Guan, Dengfeng;McCarthy, Shane A.;Durbin, Richard
动机：长读段测序和支架技术的快速发展正在加速大型真核基因组参考质量组装的生产。然而，在高杂合性区域中的单倍型趋异通常导致组装者产生两个拷贝而不是一个拷贝的区域，导致邻接性的断裂并损害下游步骤如基因注释。已经开发了几种工具来解决这个问题。然而，他们要么只专注于删除所包含的重复区域，也被称为haplotigs，或未能使用所有相关信息，因此makers.Results：在这里，我们提出了一种新的工具，purge_dups，使用序列相似性和读取深度自动识别和删除haplotigs和杂合重叠。与现有的工具相比，我们证明了purge_dups可以减少杂合重复，增加组装连续性，同时保持初级组装的完整性。此外，purge_dups是全自动的，可以很容易地集成到装配流水线中。
Motivation: Rapid development in long-read sequencing and scaffolding technologies is accelerating the production of reference-quality assemblies for large eukaryotic genomes. However, haplotype divergence in regions of high heterozygosity often results in assemblers creating two copies rather than one copy of a region, leading to breaks in contiguity and compromising downstream steps such as gene annotation. Several tools have been developed to resolve this problem. However, they either focus only on removing contained duplicate regions, also known as haplotigs, or fail to use all the relevant information and hence make errors.Results: Here we present a novel tool, purge_dups, that uses sequence similarity and read depth to automatically identify and remove both haplotigs and heterozygous overlaps. In comparison with current tools, we demonstrate that purge_dups can reduce heterozygous duplication and increase assembly continuity while maintaining completeness of the primary assembly. Moreover, purge_dups is fully automatic and can easily be integrated into assembly pipelines.