RAmbler resolves complex repeats in human Chromosomes 8, 19, and X.

ABSTRACT: Repetitive regions in eukaryotic genomes often contain important functional or regulatory elements. Despite significant algorithmic and technological advancements in genome sequencing and assembly over the past three decades, modern de novo assemblers still struggle to accurately reconstruct highly repetitive regions. In this work, we introduce RAmbler (Repeat Assembler), a reference-guided assembler specialized for the assembly of complex repetitive regions exclusively from Pacific Biosciences (PacBio) HiFi reads. RAmbler (1) identifies repetitive regions by detecting unusually high coverage regions after mapping HiFi reads to the draft genome assembly, (2) finds single-copy k-mers from the HiFi reads, (i.e., k-mers that are expected to occur only once in the genome), (3) us

SUBMITTER: Chakravarty S 

PROVIDER: S-EPMC12047272 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature