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Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

2021; Nature Portfolio; Volume: 18; Issue: 2 Linguagem: Inglês

10.1038/s41592-020-01056-5

1548-7105

Haoyu Cheng, Gregory T. Concepcion, Xiaowen Feng, Haowen Zhang, Heng Li,

Genetic diversity and population structure

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 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 nonhuman datasets, including California redwood with a ~30-Gb hexaploid genome, we show that hifiasm frequently delivers better assemblies than existing tools and consistently outperforms others on haplotype-resolved assembly. Hifiasm is a haplotype-resolved de novo genome assembler for long-read high-fidelity sequencing data based on phased assembly graphs.