Assembly-graph-assisted haplotype-resolved scaffolding of polyploid genomes.

GPhase significantly improves haplotype-resolved scaffolding of complex polyploid genomes, reducing sequence missing rate by up to tens-fold and error rate by up to an order of magnitude.

• Why it matters: Assembling high-quality, chromosome-level polyploid genomes remains difficult due to challenges in distinguishing homologous chromosomes and resolving complex regions, leaving many species without complete sequences. Improving assembly accuracy and completeness is essential for advancing genomic research and understanding polyploid biology.
• What they did: The study developed GPhase, a scaffolding algorithm that combines 3C data (such as Hi-C, Pore-C, and Omni-C) with assembly graphs, leveraging long-read overlaps to enhance phasing and contiguity. The approach was applied to 15 complex polyploid genomes.
• The result: GPhase outperformed existing tools by reducing sequence missing rates, decreasing error rates, and increasing contiguity (N50), enabling more accurate and complete polyploid genome assemblies.