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

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Repetitive genomic regions are crucial for function and regulation but challenging to assemble.
• Despite advances, de novo assemblers struggle with accurate reconstruction of these complex areas.

Purpose of the Study:

• Introduce RAmbler, a specialized assembler for complex repetitive regions.
• Utilize Pacific Biosciences (PacBio) HiFi reads for high-accuracy genome assembly.

Main Methods:

• RAmbler identifies repeats via high-coverage mapping and single-copy k-mer analysis.
• Reads are barcoded using k-mer locations, then clustered based on shared barcodes.
• Contigs are generated per cluster, followed by consensus assembly.

Main Results:

• RAmbler achieves assembly quality comparable to manually curated human genome assemblies for centromeres and complex repeats.
• Outperforms hifiasm, LJA, HiCANU, and Verkko on diverse synthetic datasets.
• Demonstrates robust performance across varying repeat lengths, numbers, heterozygosity, and sequencing depths.

Conclusions:

• RAmbler offers a significant advancement in assembling challenging repetitive genomic elements.
• Provides a high-quality solution for complex repeat reconstruction using PacBio HiFi data.