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

Published

May 4, 2020

Author(s)

Justin M. Zook, Kishwar Shafin, Trevor Pesout, Ryan Lorig-Roach, Marina Haukness, Hugh E. Olsen, Miten Jain, Benedict Paten

Abstract

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 63x coverage, 42-kb read N50 values and 6.5x 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.

Citation

Nature Biotechnology

Volume

38

Pub Type

Journals

Download Paper

https://doi.org/10.1038/s41587-020-0503-6

Local Download

Keywords

Nanopore, Assembly, Polishing, PromethION, Human Genomes

Citation

Zook, J. , Shafin, K. , Pesout, T. , Lorig-Roach, R. , Haukness, M. , Olsen, H. , Jain, M. and Paten, B. (2020), Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes, Nature Biotechnology, [online], https://doi.org/10.1038/s41587-020-0503-6 (Accessed January 23, 2025)