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arXiv · 2008.01237

Haplotype-resolved de novo assembly with phased assembly graphs

Haoyu Cheng·Gregory T Concepcion·Xiaowen Feng·Haowen Zhang·Heng Li
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Abstract

Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the haplotypes to produce high-quality phased assemblies. Here we describe hifiasm, a new de novo assembler that takes advantage of long high-fidelity sequence reads to faithfully represent the haplotype information in a phased assembly graph. Unlike other graph-based assemblers that only aim to maintain the contiguity of one haplotype, hifiasm strives to preserve the contiguity of all haplotypes. This feature enables the development of a graph trio binning algorithm that greatly advances over standard trio binning. On three human and five non-human datasets, including California redwood with a $\sim$30-gigabase hexaploid genome, we show that hifiasm frequently delivers better assemblies than existing tools and consistently outperforms others on haplotype-resolved assembly.

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Haoyu Cheng, Gregory T Concepcion, Xiaowen Feng, Haowen Zhang, Heng Li. 2020-08-03. Haplotype-resolved de novo assembly with phased assembly graphs. https://doi.org/10.1038/s41592-020-01056-5

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