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SVLR: Genome Structural Variant Detection Using Long-Read Sequencing Data

文献类型：期刊论文

作者Gu, Wenyan3; Zhou, Aizhong3; Wang, Lusheng2; Sun, Shiwei1; Cui, Xuefeng3; Zhu, Daming3
刊名JOURNAL OF COMPUTATIONAL BIOLOGY
出版日期2021-05-10
页码15
关键词genome structural variant genome structural variant detection long-read sequencing and single-molecule sequencing third-generation sequencing
ISSN号1066-5277
DOI10.1089/cmb.2021.0048
英文摘要Genome structural variants (SVs) have great impacts on human phenotype and diversity, and have been linked to numerous diseases. Long-read sequencing technologies arise to make it possible to find SVs of as long as 10,000 nucleotides. Thus, long read-based SV detection has been drawing attention of many recent research projects, and many tools have been developed for long reads to detect SVs recently. In this article, we present a new method, called SVLR, to detect SVs based on long-read sequencing data. Comparing with existing methods, SVLR can detect three new kinds of SVs: block replacements, block interchanges, and translocations. Although these new SVs are structurally more complicated, SVLR achieves accuracies that are comparable with those of the classic SVs. Moreover, for the classic SVs that can be detected by state-of-the-art methods (e.g., SVIM and Sniffles), our experiments demonstrate recall improvements of up to 38% without harming the precisions (i.e., >78%). We also point out three directions to further improve SV detection in the future. Source codes: https://github.com/GWYSDU/SVLR
资助项目National Science Foundation of China[61732009] ; National Science Foundation of China[61761136017] ; National Science Foundation of China[62072283]
WOS研究方向Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
语种英语
WOS记录号WOS:000649049200001
出版者MARY ANN LIEBERT, INC
源URL[http://119.78.100.204/handle/2XEOYT63/17842]  
专题中国科学院计算技术研究所期刊论文_英文
通讯作者Cui, Xuefeng; Zhu, Daming
作者单位1.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing, Peoples R China
2.City Univ Hong Kong, Dept Comp Sci, Hong Kong, Peoples R China
3.Shandong Univ, Sch Comp Sci & Technol, Qingdao 266237, Peoples R China
推荐引用方式
GB/T 7714		 Gu, Wenyan,Zhou, Aizhong,Wang, Lusheng,et al. SVLR: Genome Structural Variant Detection Using Long-Read Sequencing Data[J]. JOURNAL OF COMPUTATIONAL BIOLOGY,2021:15.
APA Gu, Wenyan,Zhou, Aizhong,Wang, Lusheng,Sun, Shiwei,Cui, Xuefeng,&Zhu, Daming.(2021).SVLR: Genome Structural Variant Detection Using Long-Read Sequencing Data.JOURNAL OF COMPUTATIONAL BIOLOGY,15.
MLA Gu, Wenyan,et al."SVLR: Genome Structural Variant Detection Using Long-Read Sequencing Data".JOURNAL OF COMPUTATIONAL BIOLOGY (2021):15.

入库方式： OAI收割

来源：计算技术研究所

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