Targeted sequencing and iterative assembly of near-complete genomes

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, Elaine Stackpoole, Lauren Roman, Luke W. Silver, Carolyn J. Hogg, Louise M. Streeting, Ozren Bogdanovic, Renata Coelho Rodrigues Noronha, Luís Adriano Santos do Nascimento, Adauto Lima Cardoso, Arthur Georges, Haoyu Cheng, Hardip R. Patel, Kishore Raj Kumar, Amali C. Mallawaarachchi and Ira W. Deveson ()
Additional contact information
Hasindu Gamaarachchi: Garvan Institute of Medical Research, Genomics and Inherited Disease Program
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
Melissa Rapadas: Garvan Institute of Medical Research, Genomics and Inherited Disease Program
Kavindu Jayasooriya: Garvan Institute of Medical Research, Genomics and Inherited Disease Program
Tonia Russell: Garvan Institute of Medical Research, Genomics and Inherited Disease Program
Dennis Yeow: Garvan Institute of Medical Research, Genomics and Inherited Disease Program
Yvonne Hort: Garvan Institute of Medical Research, Genomics and Inherited Disease Program
Chirag Patel: Royal Brisbane and Women’s Hospital, Genetic Health Queensland
Andrew J. Mallett: James Cook University, College of Medicine and Dentistry
Elaine Stackpoole: King Edward Memorial Hospital, Genetic Health Western Australia
Lauren Roman: University of Tasmania, Institute for Marine and Antarctic Studies
Luke W. Silver: The University of Sydney, School of Life and Environmental Sciences
Carolyn J. Hogg: The University of Sydney, School of Life and Environmental Sciences
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
Renata Coelho Rodrigues Noronha: National Council for Scientific and Technological Development (CNPq)
Luís Adriano Santos do Nascimento: National Council for Scientific and Technological Development (CNPq)
Adauto Lima Cardoso: CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Centro Andaluz de Biología del Desarrollo
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
Amali C. Mallawaarachchi: Garvan Institute of Medical Research, Genomics and Inherited Disease Program
Ira W. Deveson: Garvan Institute of Medical Research, Genomics and Inherited Disease Program

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: 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).

Date: 2025
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DOI: 10.1038/s41467-025-65410-x

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