Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.
Nat Biotechnol
; 38(9): 1044-1053, 2020 09.
Article
em En
| MEDLINE
| ID: mdl-32686750
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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Base de dados:
MEDLINE
Assunto principal:
Genoma Humano
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Análise de Sequência de DNA
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Sequenciamento de Nucleotídeos em Larga Escala
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Sequenciamento por Nanoporos
Limite:
Humans
Idioma:
En
Ano de publicação:
2020
Tipo de documento:
Article