Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
Kishwar Shafin, Trevor Pesout, Ryan Lorig-Roach, Marina Haukness, Hugh E. Olsen, Colleen M. Bosworth, Joel Armstrong, Kristof Tigyi, Nicholas Maurer, Sergey Koren, Fritz J. Sedlazeck, Tobias Marschall, Simon Mayes, Vânia Costa, Justin M. Zook, Kelvin J. Liu, Duncan Kilburn, Melanie Sorensen, Katherine M. Munson, Mitchell R. Vollger, Jean Monlong, Erik Garrison, Evan E. Eichler, Sofie R. Salama, David Haussler, Richard E. Green, Mark Akeson, Adam M. Phillippy, Karen H. Miga, P. Carnevali, 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 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.