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

Goodwin, S., Gurtowski, J., Ethe-Sayers, S., Deshpande, P., Schatz, M. C., McCombie, W. R. (2015) Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Res, 25 (11). pp. 1750-1756. ISSN 1088-9051

URL: http://www.ncbi.nlm.nih.gov/pubmed/26447147
DOI: 10.1101/gr.191395.115

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 approximately 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.

Item Type: Paper
Subjects: Investigative techniques and equipment
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes > de novo assembly
Investigative techniques and equipment > assays > next generation sequencing
CSHL Authors:
Communities: CSHL Cancer Center Program > Cancer Genetics
CSHL labs > McCombie lab
CSHL labs > Schatz lab
Depositing User: Matt Covey
Date Deposited: 15 Oct 2015 15:36
Last Modified: 25 Nov 2015 20:08
PMCID: PMC4617970
Related URLs:
URI: http://repository.cshl.edu/id/eprint/31924

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