Oxford Nanopore Sequencing and de novo Assembly of a Eukaryotic Genome

Monitoring the progress of DNA through a pore has been postulated as a method for sequencing DNA for several decades1,2. Recently, a nanopore instrument, the Oxford Nanopore MinION, has become available3. Here we describe our sequencing of the S. cerevisiae genome. We describe software developed to make use of these data as existing packages were incapable of assembling long reads at such high error rate (～35% error). With these methods we were able to error correct and assemble the nanopore reads de novo, producing an assembly that is contiguous and accurate: with a contig N50 length of 479kb, and has greater than 99% consensus identity when compared to the reference. The assembly with the long nanopore reads was able to correctly assemble gene cassettes, rRNAs, transposable elements, and other genomic features that were almost entirely absent in an assembly using Illumina sequencing alone (with a contig N50 of only 59,927bp).