KOREF

KOREF constructs chromosome-scale de novo human genome assemblies and compares Pacific Biosciences SMRT and Oxford Nanopore Technologies PromethION long-read sequencing platforms to evaluate assembly quality and cost-effectiveness for a Korean reference genome.

Key Features:

• Chromosome-scale de novo assembly: Whole-genome de novo assembly of the Korean genome using long-read sequencing data to produce chromosome-scale assemblies.
• Sequencing platforms and coverage: Assemblies were produced from ONT PromethION (64×, 193 Gb from three flowcells) yielding 3,725 contigs with N50 16.7 Mb and total genome length 2.8 Gb, and from PacBio SMRT (62×, 188 Gb) yielding 2,695 contigs with N50 17.9 Mb.
• Hi-C long-range mapping: Incorporation of Hi-C-derived long-range mapping data improved the PromethION 64× assembly to 3,179 scaffolds with an N50 of 56.4 Mb.
• Structural variation analysis: Use of long DNA reads to facilitate assembly and structural variation discovery compared to short-read methods.
• Cost-effectiveness comparison: Direct comparison of assembly quality and cost between PacBio SMRT and ONT PromethION, noting PacBio SMRT's higher expense relative to PromethION.

Scientific Applications:

• Korean reference genome: Generation and refinement of a high-quality Korean reference genome at chromosome scale.
• Sequencing platform benchmarking: Comparative evaluation of PacBio SMRT and ONT PromethION performance for human de novo assembly at high coverage.
• Genome assembly and SV discovery: Production of assemblies suitable for structural variation discovery and downstream genomic analyses.

Methodology:

Whole-genome de novo assemblies were generated from PacBio SMRT and ONT PromethION long-read data, assemblies were scaffolded with Hi-C-derived long-range mapping, and assemblies were compared by contig/scaffold counts, N50, and total genome length.