Targeted sequencing and iterative assembly of near-complete genomes

Recent advances in long-read sequencing (LRS) and assembly algorithms have
made it possible to create highly complete genome assemblies for humans,
animals, plants, and other eukaryotes. However, there is a need for
ongoing development to improve accessibility and affordability of the
required data, increase the range of usable sample types, and reliably
resolve the most challenging, repetitive genome regions.
'Cornetto' is a new experimental paradigm in which the genome
assembly process is adaptively integrated with programmable selective
nanopore sequencing, with target regions being iteratively updated to
focus LRS data production onto the unsolved regions of a nascent assembly.
This improves assembly quality and streamlines the process, both for human
individuals and diverse non-human vertebrates, including endemic
Australian endangered species, tested here. Cornetto enables us to
generate highly complete diploid human genome assemblies using only a
single LRS platform, surpassing the quality of previous efforts at a
fraction of the cost. Cornetto enables genome assembly from challenging
sample types like human saliva, for the first time, further enhancing
accessibility. Finally, we obtain complete and 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) - inherited diseases for
which diagnosis is complicated by an inability to sequence the genes
involved. In summary, Cornetto will improve, accelerate, and democratise
genome assembly, delivering impacts across a range of bioscience domains.