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

  • Author(s): Shafin, 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
  • et al.
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.

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