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

TLDR

Sequencing DNA by monitoring molecules through a membrane pore has been proposed for decades. The authors developed Nanocorr, a hybrid error‑correction algorithm for Oxford Nanopore reads, to enable assembly of long reads with high error rates. Nanocorr corrects Oxford Nanopore reads by integrating complementary MiSeq data, enabling de novo assembly of the Saccharomyces cerevisiae genome. Hybrid error correction with Nanocorr produced a highly contiguous and accurate assembly, with a contig N50 more than ten times that of an Illumina‑only assembly (678 kb vs 59.9 kb) and >99.88 % consensus identity, and it captured genomic features absent in Illumina‑only assemblies.

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.