TY  - JOUR
A1  - Goodwin, Sara
A1  - Gurtowski, James
A1  - Ethe-Sayers, Scott
A1  - Deshpande, Panchajanya
A1  - Schatz, Michael C.
A1  - McCombie, W. Richard
T1  - Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome
Y1  - 2015/11/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1750 
EP  - 1756 
DO  - 10.1101/gr.191395.115 
VL  - 25 
IS  - 11 
UR  - http://genome.cshlp.org/content/25/11/1750.abstract 
N2  - 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. 
ER  -