OMGS: Optical Map-based Genome Scaffolding
OMGS: Optical Map-based Genome Scaffolding
复制标题
OMGS：基于光学图谱的基因组支架
DOI：
10.1007/978-3-030-17083-7_12
复制
发表时间：
2019
期刊：
影响因子：
--
通讯作者：
W. Pan, T. Jiang
中科院分区：
文献类型：
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作者：
W. Pan, T. Jiang
由于目前测序技术的限制，从头基因组组装通常分两个阶段进行，即contig（序列）组装和scaffolding。虽然脚手架在计算上比序列组装更容易，但由于真核生物基因组的高重复内容，组装的组群中可能存在错误连接，以及链接信息的不准确性，脚手架问题可能具有挑战性。基因组脚手架工具要么使用成对末端/配偶对/连锁/Hi-C读取或全基因组图谱（光学、物理或遗传）作为连锁信息。光学图谱（特别是Bionano Genomics图谱）已广泛应用于最近的许多大规模基因组组装项目（如山羊、苹果、大麦、玉米、藜麦、海鲈鱼等）。然而，最常用的脚手架工具有一个严重的限制：它们一次只能处理一个光学地图，迫使用户交替或迭代多个地图。在本文中，我们首次提出了一种新的基于光学图谱的基因组图谱构建算法OMGS （Optical Map-based Genome scaffolding）。OMGS解决了若干优化问题，生成了最优的连续性和正确性的支架。大量的实验结果表明，当使用多个光学图时，我们的工具优于现有的方法，并且使用单个光学图产生可比的支架。
Due to the current limitations of sequencing technologies, de novo genome assembly is typically carried out in two stages, namely contig (sequence) assembly and scaffolding. While scaffolding is computationally easier than sequence assembly, the scaffolding problem can be challenging due to the high repetitive content of eukaryotic genomes, possible mis-joins in assembled contigs, and inaccuracies in the linkage information. Genome scaffolding tools either use paired-end/mate-pair/linked/Hi-C reads or genome-wide maps (optical, physical, or genetic) as linkage information. Optical maps (in particular Bionano Genomics maps) have been extensively used in many recent large-scale genome assembly projects (e.g., goat, apple, barley, maize, quinoa, sea bass, among others). However, the most commonly used scaffolding tools have a serious limitation: they can only deal with one optical map at a time, forcing users to alternate or iterate over multiple maps. In this article, we introduce a novel scaffolding algorithm called OMGS (Optical Map-based Genome Scaffolding) that for the first time can take advantages of multiple optical maps. OMGS solves several optimization problems to generate scaffolds with optimal contiguity and correctness. Extensive experimental results demonstrate that our tool outperforms existing methods when multiple optical maps are available and produces comparable scaffolds using a single optical map.