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

TitleNanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.
Publication TypeJournal Article
Year of Publication2020
AuthorsShafin, 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, Garrison, E, Eichler, EE, Salama, S, Haussler, D, Green, RE, Akeson, M, Phillippy, A, Miga, KH, Carnevali, P, Jain, M, Paten, B
JournalNat Biotechnol
Volume38
Issue9
Pagination1044-1053
Date Published2020 09
ISSN1546-1696
KeywordsAlgorithms, Benchmarking, Chromosomes, Human, Deep Learning, Genome, Human, Genomics, Haploidy, High-Throughput Nucleotide Sequencing, HLA Antigens, Humans, Nanopore Sequencing, Sequence Analysis, DNA
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.

DOI10.1038/s41587-020-0503-6
Alternate JournalNat Biotechnol
PubMed ID32686750
PubMed Central IDPMC7483855
Grant ListU01 HG010961 / HG / NHGRI NIH HHS / United States
U41 HG010972 / HG / NHGRI NIH HHS / United States
/ HHMI / Howard Hughes Medical Institute / United States
R01 HG010329 / HG / NHGRI NIH HHS / United States
U24 HG010262 / HG / NHGRI NIH HHS / United States
U01 HG010971 / HG / NHGRI NIH HHS / United States
R01 HG009737 / HG / NHGRI NIH HHS / United States
R01 HG010485 / HG / NHGRI NIH HHS / United States
OT2 OD026682 / OD / NIH HHS / United States
OT3 HL142481 / HL / NHLBI NIH HHS / United States