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Genome Res. 2015 Nov;25(11):1750-6. doi: 10.1101/gr.191395.115. Epub 2015 Oct 7.

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome.

Author information

1
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

Abstract

Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available, and we used this for sequencing the Saccharomyces cerevisiae genome. To make use of these data, we developed a novel open-source hybrid error correction algorithm Nanocorr specifically for Oxford Nanopore reads, because existing packages were incapable of assembling the long read lengths (5-50 kbp) at such high error rates (between ∼5% and 40% error). With this new method, we were able to perform a hybrid error correction of the nanopore reads using complementary MiSeq data and produce a de novo assembly that is highly contiguous and accurate: The contig N50 length is more than ten times greater than an Illumina-only assembly (678 kb versus 59.9 kbp) and has >99.88% consensus identity when compared to the reference. Furthermore, the assembly with the long nanopore reads presents a much more complete representation of the features of the genome and correctly assembles gene cassettes, rRNAs, transposable elements, and other genomic features that were almost entirely absent in the Illumina-only assembly.

PMID:
26447147
PMCID:
PMC4617970
DOI:
10.1101/gr.191395.115
[Indexed for MEDLINE]
Free PMC Article

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