Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph
文献类型：期刊论文
| 作者 | Huang,Bin1,2; Wei,Guozheng1,2; Wang,Bing1,2; Ju,Fusong1,2; Zhong,Yi3; Shi,Zhuozheng4; Sun,Shiwei1,2,5; Bu,Dongbo1,2,5 |
| 刊名 | BMC Bioinformatics
 |
| 出版日期 | 2021-10-30 |
| 卷号 | 22期号:1 |
| 关键词 | Genome assembly Gap filling Scaffolding Optical maps Probabilistic search |
| DOI | 10.1186/s12859-021-04448-2 |
| 英文摘要 | 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. |
| 语种 | 英语 |
| WOS记录号 | BMC:10.1186/S12859-021-04448-2 |
| 出版者 | BioMed Central |
| 源URL | [http://119.78.100.204/handle/2XEOYT63/17033]  |
| 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). |
入库方式： OAI收割
来源：计算技术研究所
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