Scaffolding is crucial for constructing most chromosome-level genomes. The high-throughput chromatin conformation capture (Hi-C) technology has become the primary scaffolding strategy due to its convenience and cost-effectiveness. As sequencing technologies and assembly algorithms advance, constructing haplotype-resolved genomes is increasingly preferred because haplotypes can provide additional genetic information on allelic and non-allelic variations. ALLHiC is a widely used allele-aware scaffolding tool designed for this purpose. However, its dependence on chromosome-level reference genomes and a higher chromosome misassignment rate still impede the unravelling of haplotype-resolved genomes. Here we present HapHiC, a reference-independent allele-aware scaffolding tool with superior performance on chromosome assignment as well as contig ordering and orientation. In addition, we provide new insights into the challenges in allele-aware scaffolding by conducting comprehensive analyses on various adverse factors. Finally, with the help of HapHiC, we constructed the haplotype-resolved allotriploid genome for Miscanthus × giganteus, an important lignocellulosic bioenergy crop.

支架对于构建大多数染色体水平基因组至关重要。高通量染色质构象捕获（Hi-C）技术因其便利性和成本效益而成为主要的支架策略。随着测序技术和组装算法的进步，构建单倍型解析的基因组越来越受欢迎，因为单倍型可以提供有关等位基因和非等位基因变异的额外遗传信息。 ALLHiC 是一种广泛使用的等位基因感知支架工具，专为此目的而设计。然而，它对染色体水平参考基因组的依赖和较高的染色体错配率仍然阻碍了单倍型解析基因组的解开。在这里，我们介绍 HapHiC，一种独立于参考的等位基因感知支架工具，在染色体分配以及重叠群排序和方向方面具有卓越的性能。此外，我们通过对各种不利因素进行全面分析，为等位基因感知支架的挑战提供了新的见解。最后，在 HapHiC 的帮助下，我们构建了芒草（一种重要的木质纤维素生物能源作物）的单倍型解析的异源三倍体基因组。