Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
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Open Access
- 4 May 2020
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Biotechnology
- Vol. 38 (9), 1044-1053
- https://doi.org/10.1038/s41587-020-0503-6
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 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.Keywords
Funding Information
- U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (1U01HL137183)
- U.S. Department of Health & Human Services | National Institutes of Health (5U54HG007990, 5T32HG008345-04, 1U01HL137183, R01HG010053)
- U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (3U24HG009084-03S1, 2U41HG007234)
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