  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.
