TRFill: synergistic use of HiFi and Hi-C sequencing enables accurate assembly of tandem repeats for population-level analysis
文献类型： 外文期刊
作者： Wen, Huaming 1 ; Yang, Jinbao 2 ; Zhao, Xianjia 2 ; Wang, Xingbin 2 ; Lei, Jiawei 2 ; Li, Yanchun 2 ; Du, Wenjie 2 ; Li, Dongxi 4 ; Xu, Yun 1 ; Lonardi, Stefano 3 ; Pan, Weihua 2 ;
作者机构： 1.Univ Sci & Technol China, Sch Comp Sci & Technol, Hefei 230027, Peoples R China
2.Chinese Acad Agr Sci, State Key Lab Genome & Multiom Technol, Genome Anal Lab,Minist Agr & Rural Affairs,Agr Gen, Shenzhen Branch,Guangdong Lab Lingnan Modern Agr, Shenzhen 518120, Peoples R China
3.Univ Calif Riverside, Dept Comp Sci & Engn, Riverside, CA 92521 USA
4.Taiyuan Univ Technol, Coll Comp Sci & Technol, Taiyuan 030024, Peoples R China
关键词： Genome assembly; Gap filling; Reference-guided genome assembly; Tandem repeats; Segmental duplications
期刊名称：GENOME BIOLOGY （ 影响因子：9.4； 五年影响因子：16.3 ）
ISSN： 1474-760X
年卷期： 2025 年 26 卷 1 期
页码：
收录情况： SCI
摘要： The highly repetitive content of eukaryotic genomes, including long tandem repeats, segmental duplications, and centromeres, makes haplotype-resolved genome assembly hard. Repeat sequences introduce gaps or mis-joins in the assemblies. We introduce TRFill, a novel algorithm that can close the gaps in a draft chromosome-level assembly using exclusively PacBio HiFi and Hi-C data. Experimental results on human centromeres and tomato subtelomeres show that TRFill can improve the completeness and correctness of about two-thirds of the tandem repeats. We also show that the improved completeness of subtelomeric tandem repeats in the tomato pangenome enables a population-level analysis of these complex repeats.
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