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Targeted sequencing and iterative assembly of near-complete genomes

Author

Listed:
  • Hasindu Gamaarachchi

    (Garvan Institute of Medical Research, Genomics and Inherited Disease Program
    University of New South Wales, School of Computer Science and Engineering)

  • Igor Stevanovski

    (Garvan Institute of Medical Research, Genomics and Inherited Disease Program)

  • Jillian M. Hammond

    (Garvan Institute of Medical Research, Genomics and Inherited Disease Program)

  • Andre L. M. Reis

    (Garvan Institute of Medical Research, Genomics and Inherited Disease Program
    University of New South Wales, Faculty of Medicine and Health, St Vincent’s Healthcare Clinical Campus)

  • Melissa Rapadas

    (Garvan Institute of Medical Research, Genomics and Inherited Disease Program)

  • Kavindu Jayasooriya

    (Garvan Institute of Medical Research, Genomics and Inherited Disease Program
    University of New South Wales, School of Computer Science and Engineering)

  • Tonia Russell

    (Garvan Institute of Medical Research, Genomics and Inherited Disease Program)

  • Dennis Yeow

    (Garvan Institute of Medical Research, Genomics and Inherited Disease Program
    Concord Repatriation General Hospital, Molecular Medicine Laboratory and Neurology Department
    University of Sydney, Faculty of Medicine and Health
    Prince of Wales Hospital, Neurodegenerative Service)

  • Yvonne Hort

    (Garvan Institute of Medical Research, Genomics and Inherited Disease Program)

  • Chirag Patel

    (Royal Brisbane and Women’s Hospital, Genetic Health Queensland
    The University of Queensland, Faculty of Health, Medicine and Behavioural Sciences)

  • Andrew J. Mallett

    (James Cook University, College of Medicine and Dentistry
    Townsville University Hospital, Department of Renal Medicine
    The University of Queensland, Institute for Molecular Bioscience)

  • Elaine Stackpoole

    (King Edward Memorial Hospital, Genetic Health Western Australia)

  • Lauren Roman

    (University of Tasmania, Institute for Marine and Antarctic Studies
    CSIRO Environment)

  • Luke W. Silver

    (The University of Sydney, School of Life and Environmental Sciences
    University of Sydney, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science)

  • Carolyn J. Hogg

    (The University of Sydney, School of Life and Environmental Sciences
    University of Sydney, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science)

  • Louise M. Streeting

    (University of New England, School of Environmental and Rural Science)

  • Ozren Bogdanovic

    (University of New South Wales, School of Biotechnology and Biomolecular Sciences
    CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Centro Andaluz de Biología del Desarrollo)

  • Renata Coelho Rodrigues Noronha

    (National Council for Scientific and Technological Development (CNPq)
    Universidade Federal do Pará, Laboratório de Genética e Biologia Celular, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas)

  • Luís Adriano Santos do Nascimento

    (National Council for Scientific and Technological Development (CNPq)
    Universidade Federal do Pará, Laboratório de Genética e Biologia Celular, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas)

  • Adauto Lima Cardoso

    (CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Centro Andaluz de Biología del Desarrollo
    National Council for Scientific and Technological Development (CNPq)
    Universidade Estadual Paulista, Instituto de Biociências de Botucatu)

  • Arthur Georges

    (University of Canberra, Institute for Applied Ecology)

  • Haoyu Cheng

    (Yale School of Medicine, Department of Biomedical Informatics and Data Science)

  • Hardip R. Patel

    (Australian National University, National Centre for Indigenous Genomics, John Curtin School of Medical Research)

  • Kishore Raj Kumar

    (Garvan Institute of Medical Research, Genomics and Inherited Disease Program
    University of New South Wales, Faculty of Medicine and Health, St Vincent’s Healthcare Clinical Campus
    Concord Repatriation General Hospital, Molecular Medicine Laboratory and Neurology Department
    University of Sydney, Faculty of Medicine and Health)

  • Amali C. Mallawaarachchi

    (Garvan Institute of Medical Research, Genomics and Inherited Disease Program
    University of New South Wales, Faculty of Medicine and Health, St Vincent’s Healthcare Clinical Campus
    Royal Prince Alfred Hospital, Clinical Genetics Service, Institute of Precision Medicine and Bioinformatics)

  • Ira W. Deveson

    (Garvan Institute of Medical Research, Genomics and Inherited Disease Program
    University of New South Wales, Faculty of Medicine and Health, St Vincent’s Healthcare Clinical Campus)

Abstract

Advances in long-read sequencing (LRS) and assembly algorithms have made it possible to create highly complete genome assemblies for humans, animals and plants. However, ongoing development is needed to improve accessibility, affordability, and assembly quality and completeness. ‘Cornetto’ is a new strategy in which we use programmable selective nanopore sequencing to focus LRS data production onto the unsolved regions of a nascent assembly. This improves assembly quality and streamlines the process, both for humans and non-human vertebrates. Cornetto enables us to generate highly complete diploid human genome assemblies using only nanopore LRS data, surpassing the quality of previous efforts at a fraction of the cost. Cornetto enables genome assembly from challenging sample types like human saliva. Finally, we obtain accurate assemblies for clinically-relevant repetitive loci at the extremes of the genome, demonstrating valid approaches for genetic diagnosis in facioscapulohumeral muscular dystrophy (FSHD) and MUC1-autosomal dominant tubulointerstitial kidney disease (MUC1-ADTKD).

Suggested Citation

  • Hasindu Gamaarachchi & Igor Stevanovski & Jillian M. Hammond & Andre L. M. Reis & Melissa Rapadas & Kavindu Jayasooriya & Tonia Russell & Dennis Yeow & Yvonne Hort & Chirag Patel & Andrew J. Mallett &, 2025. "Targeted sequencing and iterative assembly of near-complete genomes," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-65410-x
    DOI: 10.1038/s41467-025-65410-x
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