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bioRxiv · 10.1101/2023.11.18.567668

Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes

Zeng, X.·Yi, Z.·Zhang, X.·Du, Y.·Li, Y.·Zhou, Z.·Chen, S.·Zhao, H.·Yang, S.·Wang, Y.·Chen, G.
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Abstract

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 unraveling of haplotype-resolved genomes. In this paper, we present HapHiC, a reference-independent allele-aware scaffolding tool with superior performance on chromosome assignment as well as contig ordering and orientation. Additionally, 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 x giganteus, an important lignocellulosic bioenergy crop. HapHiC is available at https://github.com/zengxiaofei/HapHiC.

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Zeng, X., Yi, Z., Zhang, X., Du, Y., Li, Y., Zhou, Z., Chen, S., Zhao, H., Yang, S., Wang, Y., Chen, G.. 2023-11-18. Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes. https://doi.org/10.1101/2023.11.18.567668

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