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Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomesShafin, Kishwar; Pesout, Trevor; Lorig-Roach, Ryan; Haukness, Marina; Olsen, Hugh E; Bosworth, Colleen; Armstrong, Joel; Tigyi, Kristof; Maurer, Nicholas; Koren, Sergey; Sedlazeck, Fritz J; Marschall, Tobias; Mayes, Simon; Costa, Vania; Zook, Justin M; Liu, Kelvin J; Kilburn, Duncan; Sorensen, Melanie; Munson, Katy M; Vollger, Mitchell R; Monlong, Jean; Garrison, Erik; Eichler, Evan E; Salama, Sofie; Haussler, David; Green, Richard E; Akeson, Mark; Phillippy, Adam; Miga, Karen H; Carnevali, Paolo; Jain, Miten; Paten, Benedict
Nature biotechnology, 09/2020, Volume: 38, Issue: 9Journal Article
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.
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