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

By Haoyu Cheng, G. Concepcion, Xiaowen Feng, Haowen Zhang, Heng Li. Nature Methods, 2021

4,997 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/788f8a32ed116f928f3cab554c6efd55385f2a80

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Citations in the corpus

A draft human pangenome reference (2022, methodology): “Trio-Hifiasm uses PacBio HiFi long-reads and parental Illumina short-reads to produce near fully phased contig assemblies.”
NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads (2024, methodology): “24) asm-gene function [4] for the human assemblies.”
Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs (2022, background): “…in 2014 (http://lh3.github.io/2014/07/19/a-proposal-of-the-grapical-fragment-assembly-format), can be used to conveniently store and visualize [8] key features of sequence graphs, such as the product of an assembly [9], the representation of variation in genomes or overlaps between reads.”
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads (2023, neutral): “The readset is then assembled with Hifiasm [9] and assembled contigs are parsed through a series of filters to yield final mitochondrial genome candidates.”