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.
journal_name
Nat Biotechnoljournal_title
Nature biotechnologyauthors
Shafin K,Pesout T,Lorig-Roach R,Haukness M,Olsen HE,Bosworth C,Armstrong J,Tigyi K,Maurer N,Koren S,Sedlazeck FJ,Marschall T,Mayes S,Costa V,Zook JM,Liu KJ,Kilburn D,Sorensen M,Munson KM,Vollger MR,Monlong J,Gardoi
10.1038/s41587-020-0503-6subject
Has Abstractpub_date
2020-09-01 00:00:00pages
1044-1053issue
9eissn
1087-0156issn
1546-1696pii
10.1038/s41587-020-0503-6journal_volume
38pub_type
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