HG002 Gradient Test

<p dir="ltr">To systematically evaluate the performance of various chromatin conformation capture technologies and 3D scaffolding algorithms at the telomere-to-telomere (T2T) level, we utilized the published high-quality Hg002(mat) T2T reference genome (doi.org/10.1016/j.cell.2026.06.016) as the gold standard. The original T2T genome was computationally fragmented into simulated contigs with three length gradients: 1 Mb, 2 Mb, and 5 Mb.

Utilizing the publicly available human HiFi-C sequencing dataset (ncbi.nlm.nih.gov/sra/ERR14275147), chromosome-level scaffolding was independently performed using three tools: wf-pore-C, CPhasing, and 3D-HiFi. Finally, the resulting scaffolds were aligned against the original T2T reference genome via whole-genome alignment to rigorously assess and validate the scaffolding accuracy and robustness across different contig continuities.</p>