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 t..., , # Targeted sequencing and iterative assembly of near-complete genomes

Dataset DOI: [10.5061/dryad.kkwh70sfr](https://doi.org/10.5061/dryad.kkwh70sfr)

## Description of the data and file structure

These assemblies were generated using the cornetto adaptive sampling method described in our manuscript. The documentation and source code used for the process are available at [https://github.com/hasindu2008/cornetto](https://github.com/hasindu2008/cornetto).

There are three files, namely cornetto-hg002-asm.tar.gz, cornetto-animal-asm.tar.gz and cornetto-hg002-asm-updates.tar.gz that are described below.

### File: cornetto-hg002-asm.tar.gz

**Description:** This tarball contains the FASTA assemblies for the hg002 sample.The below files are found inside the cornetto-hg002-asm directory created when you download and extract the cornetto-hg002-asm.tar.gz

| Assembly name | Assembly Description ..., , **Changes after Jul 16, 2025:** 

Added cornetto-hg002-asm-updates.tar.gz. The updated assemblies used in the updated version of the manuscript preprint (and the published paper).