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
第一作者： Wen, Huaming
作者： Wen, Huaming;Xu, Yun;Wen, Huaming;Yang, Jinbao;Zhao, Xianjia;Wang, Xingbin;Lei, Jiawei;Li, Yanchun;Du, Wenjie;Pan, Weihua;Lonardi, Stefano;Li, Yanchun;Li, Dongxi
作者机构：
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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