TRFill: synergistic use of HiFi and Hi-C sequencing enables accurate assembly of tandem repeats for population-level analysis

TRFill: synergistic use of HiFi and Hi-C sequencing enables accurate assembly of tandem repeats for population-level analysis

Abstract 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 t...

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Bibliographic Details
Main Authors: Huaming Wen, Jinbao Yang, Xianjia Zhao, Xingbin Wang, Jiawei Lei, Yanchun Li, Wenjie Du, Dongxi Li, Yun Xu, Stefano Lonardi, Weihua Pan
Format: Article
Language:English
Published: BMC 2025-07-01
Series:Genome Biology
Subjects:
Genome assembly
Gap filling
Reference-guided genome assembly
Tandem repeats
Segmental duplications
Online Access:https://doi.org/10.1186/s13059-025-03685-5
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