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

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 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.

SUBMITTER: Cheng H

PROVIDER: S-EPMC7961889 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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

Cheng Haoyu H Concepcion Gregory T GT Feng Xiaowen X Zhang Haowen H Li Heng H

Nature methods 20210201 2

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 assembl ...[more]

PMID: 33526886

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