期刊
NATURE METHODS
卷 18, 期 2, 页码 170-+出版社
NATURE RESEARCH
DOI: 10.1038/s41592-020-01056-5
关键词
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资金
- US National Institutes of Health [R01HG010040, U01HG010961, U41HG010972]
hifiasm is a novel assembler that utilizes long high-fidelity sequence reads to accurately represent haplotype information, outperforming existing tools in haplotype-resolved assembly on various datasets, including a hexaploid genome dataset.
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 similar to 30-Gb 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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