Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph

doi:10.1186/s12859-021-04448-2

	Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph
	Huang,Bin 1,2; Wei,Guozheng 1,2; Wang,Bing 1,2; Ju,Fusong 1,2; Zhong,Yi 3; Shi,Zhuozheng 4; Sun,Shiwei 1,2,5; Bu,Dongbo 1,2,5
	2021-10-30
发表期刊	BMC Bioinformatics
卷号	22 期号:1
摘要	AbstractBackgroundOptical maps record locations of specific enzyme recognition sites within long genome fragments. This long-distance information enables aligning genome assembly contigs onto optical maps and ordering contigs into scaffolds. The generated scaffolds, however, often contain a large amount of gaps. To fill these gaps, a feasible way is to search genome assembly graph for the best-matching contig paths that connect boundary contigs of gaps. The combination of searching and evaluation procedures might be “searching followed by evaluation”, which is infeasible for long gaps, or “searching by evaluation”, which heavily relies on heuristics and thus usually yields unreliable contig paths.ResultsWe here report an accurate and efficient approach to filling gaps of genome scaffolds with aids of optical maps. Using simulated data from 12 species and real data from 3 species, we demonstrate the successful application of our approach in gap filling with improved accuracy and completeness of genome scaffolds.ConclusionOur approach applies a sequential Bayesian updating technique to measure the similarity between optical maps and candidate contig paths. Using this similarity to guide path searching, our approach achieves higher accuracy than the existing “searching by evaluation” strategy that relies on heuristics. Furthermore, unlike the “searching followed by evaluation” strategy enumerating all possible paths, our approach prunes the unlikely sub-paths and extends the highly-probable ones only, thus significantly increasing searching efficiency.
关键词	Genome assembly Gap filling Scaffolding Optical maps Probabilistic search
DOI	10.1186/s12859-021-04448-2
语种	英语
WOS记录号	BMC:10.1186/s12859-021-04448-2
出版者	BioMed Central
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/17034
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Bu,Dongbo
作者单位	1.Chinese Academy of Sciences; Key Lab of Intelligent Information Processing, Big-Data Academy, Institute of Computing Technology 2.University of Chinese Academy of Sciences; Institute of Biology 3.University of Washington; School of Computer Science 4.University of California, San Diego; Department of Computer Science and Engineering 5.Zhongke Big Data Academy
推荐引用方式 GB/T 7714	Huang,Bin,Wei,Guozheng,Wang,Bing,et al. Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph[J]. BMC Bioinformatics,2021,22(1).
APA	Huang,Bin.,Wei,Guozheng.,Wang,Bing.,Ju,Fusong.,Zhong,Yi.,...&Bu,Dongbo.(2021).Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph.BMC Bioinformatics,22(1).
MLA	Huang,Bin,et al."Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph".BMC Bioinformatics 22.1(2021).