Haplotype-resolved assembly of diploid genomes without parental data

By Haoyu Cheng, Erich D. Jarvis, O. Fedrigo, Klaus‐Peter Koepfli, L. Urban, Neil J. Gemmell, Heng Li. Nature Biotechnology, 2022

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Routine haplotype-resolved genome assembly from single samples remains an unresolved problem. Here we describe an algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction data to produce a haplotype-resolved assembly without the sequencing of parents. Applied to human and other vertebrate samples, our algorithm consistently outperforms existing single-sample assembly pipelines and generates assemblies of similar quality to the best pedigree-based assemblies. Haplotype-resolved genome assemblies are generated by combining HiFi reads with Hi-C long-range interactions.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/2aa52f00a08b981e6e383e3b45c66823a16f41db