Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

By Kishwar Shafin, Trevor Pesout, Ryan Lorig-Roach, Marina Haukness, Hugh E. Olsen, Colleen M. Bosworth, J. Armstrong, Kristof Tigyi, Nicholas W. Maurer, Sergey Koren and 22 more. Nature Biotechnology, 2020

428 citations recorded by the source corpus.

De novo assembly of a human genome using nanopore long-read sequences has been reported, but it used more than 150,000 CPU hours and weeks of wall-clock time. To enable rapid human genome assembly, we present Shasta, a de novo long-read assembler, and polishing algorithms named MarginPolish and HELEN. Using a single PromethION nanopore sequencer and our toolkit, we assembled 11 highly contiguous human genomes de novo in 9 d. We achieved roughly 63× coverage, 42-kb read N50 values and 6.5× coverage in reads >100 kb using three flow cells per sample. Shasta produced a complete haploid human genome assembly in under 6 h on a single commercial compute node. MarginPolish and HELEN polished haploid assemblies to more than 99.9% identity (Phred quality score QV = 30) with nanopore reads alone. Addition of proximity-ligation sequencing enabled near chromosome-level scaffolds for all 11 genomes. We compare our assembly performance to existing methods for diploid, haploid and trio-binned human samples and report superior accuracy and speed. High contiguity human genomes can be assembled de novo in 6 h using nanopore long-read sequences and the Shasta toolkit.

Subfields: Artificial Intelligence, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/f9d407ce133ec096ab4321e6d98e8f0081f5bdcc

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Citations in the corpus

Symphonizing pileup and full-alignment for deep learning-based long-read variant calling (2021, methodology): “…11 , so it can better demonstrate the speed and performance of different variant calling methods, and 2) data compatibility - as at the completion date of this paper, Guppy 4 base-called reads were still the latest version available for download by the Human Pangenome Reference Consortium 12 .”
Time- and memory-efficient genome assembly with Raven (2021, methodology): “Details of the computational cost of each assembler are provided in Supplementary Table 1.”
Long-read human genome sequencing and its applications (2020, neutral): “Our findings are consistent with previous reports 34,36,56 .”
NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads (2024, background): “Each individual contained approximately 12,615 (~ 0.49 × in coverage) ultra-long reads (> 100 kb), which enabled a contiguous assembly of complex regions in the human genome [7, 8, 10, 23].”
Detection of mosaic and population-level structural variants with Sniffles2 (2024, neutral): “Sniffles2 remains open source (MIT license) and is available at https://github.com/fritzsedlazeck/Sniffles.”
A draft human pangenome reference (2022, methodology): “This is the largest set of fully phased genome assemblies currently available, outperforming earlier efforts on many levels of assembly quality (Audano et al., 2019; Ebert et al., 2021; Shafin et al., 2020).”
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads (2020, methodology): “Although the resulting read lengths are modest by the modern long-read sequencing standards — PacBio CLR reads frequently exceed 50 kbp, and ultralong Oxford Nanopore Technologies (ONT) reads can exceed even 100 kbp (Jain et al. 2018b), HiFi is a major leap forward in terms of long-read read accurac”
Nanopore sequencing technology, bioinformatics and applications (2021, neutral): “Only three PromethION flow cells were required to sequence the human genome, requiring <6 h for the computational assembly 164 .”