Haplotype-resolved de novo assembly with phased assembly graphs

2020/08/03 by Haoyu Cheng, Gregory T. Concepcion, Gregory T Concepcion +3 · 381 citations
Biochemistry, Genetics and Molecular Biology · #Genetic Associations and Epidemiology #Genetic Mapping and Diversity in Plants and Animals #Genomics and Phylogenetic Studies #q-bio.GN #q-bio.QM

paper · pdf · doi:10.1038/s41592-020-01056-5

published as Nature Methods, 2021 · 11 pages, 3 figures, 3 tables

arxiv created 2020/08/03 · openalex created_date 2020/08/10 · crossref issued 2021/02/01 · crossref published 2021/02/01 · crossref published-online 2021/02/01 · crossref published-print 2021/02/01 · openalex publication_date 2021/02/01 · crossref created 2021/02/01 · arxiv updated 2021/02/03 · crossref deposited 2023/10/19 · crossref indexed 2026/07/30 · openalex updated_date 2026/07/31

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 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 ∼30-gigabase hexaploid genome, we show that hifiasm frequently delivers better assemblies than existing tools and consistently outperforms others on haplotype-resolved assembly.

Citations

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• A chromosome-level genome assembly of the forked fungus beetle Bolitotherus cornutus , a model system for studying social evolution in the wild
• Genome assembly of the dyeing poison frog provides insights into the dynamics of transposable element and genome-size evolution
• Construction of the super pan-genome for the genus Actinidia reveals structural variations linked to phenotypic diversity
• A reference genome assembly for the pink volcano barnacle, Tetraclita rubescens , Nilsson-Cantell, 1931
• A telomere-to-telomere gapless genome reveals SlPRR1 control of circadian rhythm and photoperiodic flowering in tomato
• Sharks and rays have the oldest vertebrate sex chromosome with unique sex determination mechanisms
• Potato dihaploids uncover diverse alleles to facilitate diploid potato breeding
• Genomic insights into the domestication and genetic basis of yield in papaya
• Haplotype-resolved T2T gap-free genomes of the winegrape cultivar ‘Cabernet Sauvignon’
• PISAD: reference-free intraspecies sample anomalies detection tool based on k-mer counting
• The origin of the octoploid cloudberry ( Rubus chamaemorus ) genome is the result of multiple and complex polyploidization events
• A transposable element insertion in AUX/IAA16 disrupts splicing and causes auxin resistance in Bassia scoparia
• A chromosomal level genome assembly of Nguni Sheep, Ovis aries
• Developing future resilience from signatures of adaptation across the sorghum pangenome
• Extreme somatic mutation variation through time and space in walnut clones
• Overcoming breeding constraints in polyploid oat from evolutionary insights
• Graph pangenome reveals structural variation dynamics during cucumber breeding
• SVPG: A pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples
• Near-gapless genome assemblies of the domestic cat ( Felis silvestris catus ) and the African serval ( Leptailurus serval ) derived from trio-binning
• Two genomes of the white perch ( Morone americana ), an ecologically important teleost
• A near chromosome-level assembly of the serpentine endemic columbine, Aquilegia eximia
• Comparison of whole-genome assemblies of European river lamprey ( Lampetra fluviatilis ) and brook lamprey ( Lampetra planeri )
• The architecture of resilience: a genome assembly of Myrothamnus flabellifolia sheds light on desiccation tolerance and sex determination
• Speciation Genomics in the Tiger Whiptail Lizards ( Aspidoscelis tigris Complex)
• Topological Approaches in Animal Comparative Genomics
• From macro to micro: De novo genomes of Aedes mosquitoes enable comparative genomics among close and distant relatives
• Structural genomic variation and behavioral interactions underpin a balanced sexual mimicry polymorphism
• A near telomere-to-telomere genome assembly of the Jinhua pig: enabling more accurate genetic research
• Spiral phyllotaxis predicts left-right asymmetric growth and style deflection in mirror-image flowers of Cyanella alba
• The telomere-to-telomere genome of Pucai () ( Typha angustifolia L.): a distinctive semiaquatic vegetable with lignin and chlorophyll as quality characteristics
• Pangenome analysis provides insights into the evolution of mango ( Mangifera spp.)
• High-quality metagenome assembly from nanopore reads with nanoMDBG
• Genomics Research on the Road of Studying Biology and Virulence of Cereal Rust Fungi
• A chromosome-level reference genome facilitates the discovery of clubroot-resistant gene Crr5 in Chinese cabbage
• Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References
• Chromosomal fusions and evolutionary forces: Exploring the neo-sex chromosome system of Anolis distichus
• Extensive Recombination Suppression and Genetic Degeneration of a Young ZW Sex Chromosome System in Halfbeak Fish
• Comparative Genomics of Transisthmian Damselfishes ( Abudefduf saxatilis and A. troschelii )
• Chromosomal‐scale genome assembly of Dendrobium tangerinum provides new insights into orchid genome resources
• Moderate introgression in a single individual genome is sufficient to mislead phylogenomic inference of Triplophysa
• Parameterizing Pantherinae: De Novo Mutation Rate Estimates from Panthera and Neofelis Pedigrees
• Diploid chromosome-level genome assembly and annotation for Lycorma delicatula
• Chromosome-level phased genome assembly of the argan tree Sideroxylon spinosum L
• Improving hifiasm haplotypes for autopolyploid genome assemblies using constraint programming
• Recent Advances in Genome Editing and Bioinformatics: Addressing Challenges in Genome Editing Implementation and Genome Sequencing
• THE HAPLOTYPE-RESOLVED AND CHROMOSOME-SCALE GENOME OF VACCINIUM STAMINEUM: A NEW SOURCE OF GENETIC VARIABILITY FOR BLUEBERRY BREEDING
• Telomere-to-telomere, gap-free genome of mung bean ( Vigna radiata ) provides insights into domestication under structural variation
• Genome Sequencing of Chinese yam ( Dioscorea polystachya ): analysis of PEBP gene family diversity and identification of a potential tuber inducing factor.
• Haplotype-resolved and chromosome-level reference genome assembly of Diospyros deyangensis provides insights into the evolution and juvenile growth of persimmon
• De novo genome assembly of white clover (Trifolium repens L.) reveals the role of copy number variation in rapid environmental adaptation
• Phased T2T genome assemblies facilitate the mining of disease-resistance genes in Vitis davidii
• Genomic evidence for hybridization and introgression between blue peafowl and endangered green peafowl and molecular foundation of leucistic plumage of blue peafowl
• An Asynchronous Distributed-Memory Parallel Algorithm for k-mer Counting
• Telomere to telomere flax (Linum usitatissimum L.) genome assembly unlocks insights beyond fatty acid metabolism pathways
• The mutational dynamics of the Arabidopsis centromeres
• Beyond Genetic Indicators: How Reproductive Mode and Hybridisation Challenge Freshwater Mussel Conservation
• Rapid and dynamic evolution of a giant Y chromosome in Silene latifolia
• Minimizing detection bias of somatic mutations in a highly heterozygous oak genome
• A high-quality assembly revealing the PMEL gene for the unique plumage phenotype in Liancheng ducks
• Insights from the timber rattlesnake (Crotalus horridus) genome for MHC gene architecture and evolution in threatened rattlesnakes
• Green Elegance T2T: An upgraded telomere-to-telomere genome assembly and annotation of looseleaf lettuce ( Lactuca sativa var. crispa )
• Multiple deletions of candidate effector genes lead to the breakdown of partial grapevine resistance to downy mildew
• High-speed whole-genome sequencing of a Whippet: Rapid chromosome-level assembly and annotation of an extremely fast dog’s genome
• Three Novel Spider Genomes Unveil Spidroin Diversification and Hox Cluster Architecture: Ryuthela nishihirai (Liphistiidae), Uloborus plumipes (Uloboridae) and Cheiracanthium punctorium (Cheiracanthiidae)
• A chromosome-level genome assembly for the desert scorpion Mesobuthus przewalskii from Asian drylands
• An unusually large genome from an unusually large stonefly: A chromosome-length genome assembly for the giant salmonfly, Pteronarcys californica (Plecoptera: Pteronarcyidae)
• A chromosome-level genome assembly of the common eider, Somateria mollissima (Linnaeus, 1758)
• Revisiting pangenome openness with k-mers
• A draft reference genome assembly of California Pipevine, Aristolochia californica Torr.
• Chromosomal-level genome assembly and single-nucleotide polymorphism sites of black-faced spoonbill Platalea minor
• Genomic insights into the critically endangered King Island scrubtit
• Genome assembly of the milky mangrove Excoecaria agallocha
• Genome assembly of the edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae)
• Chromosome-level genome assembly of the common chiton, Liolophura japonica (Lischke, 1873)
• Chromosomal-level genome assembly of golden birdwing Troides aeacus (Felder & Felder, 1860)
• Comparative analyses of the banded alder borer (Rosalia funebris) and Asian longhorned beetle (Anoplophora glabripennis) genomes reveal significant differences in genome architecture and gene content among these and other Cerambycidae
• A reference genome of Commelinales provides insights into the commelinids evolution and global spread of water hyacinth (Pontederia crassipes)
• A chromosome-level genome assembly for the dugong (Dugong dugon)
• The de novo genome of the Black-necked Snakefly (Venustoraphidia nigricollis Albarda, 1891): A resource to study the evolution of living fossils
• Reference genome for the Mojave poppy bee (Perdita meconis), a specialist pollinator of conservation concern
• Newly Sequenced Genomes Reveal Patterns of Gene Family Expansion in Select Dragonflies (Odonata: Anisoptera)
• The genome of the invasive and broadly polyphagous Diaprepes root weevil, Diaprepes abbreviatus (Coleoptera), reveals an arsenal of putative polysaccharide-degrading enzymes
• Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes
• Population-level genomic analysis of immunoglobulin loci variation in rhesus macaques reveals extensive germline diversity
• A global view of human centromere variation and evolution
• Replicate avian hybrid zones reveal the progression of genetic and trait introgression through time
• Accelerating minimap2 for long-read sequencing applications on modern CPUs
• The genome of Citrus australasica reveals disease resistance and other species specific genes
• The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features
• Chromosome-Level Genome Assembly and Annotation of the Amur Rat Snake Elaphe schrenckii
• The Cathaya argyrophylla Genome Reveals the Evolutionary Trade-offs of a Living Fossil
• Supregraph: Enabling Information-Optimal Assembly Graph Representation of a Read Set
• A haplotype-resolved chromosomal reference genome for the porcini mushroom Boletus edulis
• Genome sequencing and multi-stage, blood-feeding, and tissue-specific transcriptome atlas of the Rocky Mountain wood tick provide a critical resource for this vector
• An exceptionally large, intron-rich mitochondrial genome and complex RNA processing in the desert-dwelling fungus Helvella bachu
• Nearly telomere-to-telomere genome assembly of the L. edodes diploid genome