Skip to main content
U.S. flag

An official website of the United States government

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

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



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


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.
Nature Biotechnology


Nanopore, Assembly, Polishing, PromethION, Human Genomes


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], (Accessed April 25, 2024)
Created May 3, 2020, Updated March 1, 2021