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

TLDR

De novo assembly of a human genome using nanopore long reads has been reported, but it required over 150,000 CPU hours and weeks of wall‑clock time. The authors present Shasta, a de novo long‑read assembler, together with MarginPolish and HELEN polishing algorithms, to enable rapid human genome assembly. The toolkit employs the Shasta assembler and MarginPolish/HELEN polishing, and its performance is benchmarked against existing diploid, haploid, and trio‑binned assembly methods, showing superior accuracy and speed. Using a single PromethION sequencer and the Shasta toolkit, the authors assembled 11 human genomes in 9 days with ~63× coverage and 42‑kb read N50, produced complete haploid assemblies in under 6 h, polished them to >99.9 % identity, and achieved near chromosome‑level scaffolds via proximity‑ligation sequencing, outperforming existing methods in accuracy and speed.

Abstract

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.