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. (November 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

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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:	Schatz, Michael C. McCombie, W. Richard Gurtowski, James Goodwin, Sara Deshpande, Panchajanya Ethe-Sayers, Scott
Communities:	CSHL Cancer Center Program > Cancer Genetics CSHL labs > McCombie lab CSHL labs > Schatz lab CSHL Cancer Center Program > Cancer Genetics and Genomics Program
Depositing User:	Matt Covey
Date:	November 2015
Date Deposited:	15 Oct 2015 15:36
Last Modified:	03 Nov 2020 14:31
PMCID:	PMC4617970
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/31924

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