Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
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Published:2020-05-04
Issue:9
Volume:38
Page:1044-1053
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ISSN:1087-0156
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Container-title:Nature Biotechnology
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language:en
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Short-container-title:Nat Biotechnol
Author:
Shafin KishwarORCID, Pesout Trevor, Lorig-Roach Ryan, Haukness Marina, Olsen Hugh E., Bosworth Colleen, Armstrong Joel, Tigyi Kristof, Maurer NicholasORCID, Koren SergeyORCID, Sedlazeck Fritz J.ORCID, Marschall TobiasORCID, Mayes Simon, Costa Vania, Zook Justin M., Liu Kelvin J.ORCID, Kilburn Duncan, Sorensen Melanie, Munson Katy M.ORCID, Vollger Mitchell R.ORCID, Monlong Jean, Garrison Erik, Eichler Evan E., Salama Sofie, Haussler David, Green Richard E., Akeson MarkORCID, Phillippy AdamORCID, Miga Karen H., Carnevali Paolo, Jain MitenORCID, Paten BenedictORCID
Abstract
AbstractDe 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.
Funder
U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute U.S. Department of Health & Human Services | National Institutes of Health U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute
Publisher
Springer Science and Business Media LLC
Subject
Biomedical Engineering,Molecular Medicine,Applied Microbiology and Biotechnology,Bioengineering,Biotechnology
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