Cotton 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 cotton T2T reference genome (nature.com/articles/s41588-025-02130-4) 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 cotton Pore-C sequencing dataset (onlinelibrary.wiley.com/doi/full/10.1111/pbi.13877), 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>