Alignment, error correction and assembly of a eukaryote genome

Here we present our experiences working with MinION device. We discuss the performance, tools and algorithms available for downstream analysis; including alignment methods and parameters. Our interest in the MinION device is its ability to generate long reads for complex genome assembly. Using our hybrid error correction approach called Nanocorr, we filtered the reads to optimize length and quality and corrected errors in the Oxford Nanopore reads using high identity MiSeq reads collected from the same strain. We generated 28X coverage of the genome with reads >7kb. The process improved the raw nanopore reads with a mean accuracy of ~65% to an average per base identity of 97%. The corrected reads were then assembled using the Celera Assembler which now supports reads up to 500kbp. The assembly had an average identity of 99.78% and an N50 value of 585kb. We also highlight the utility of the corrected nanopore assembly by showing that the long reads generated by the MinION are superior to MiSeq short reads in detecting complex genomic elements larger than 1300bp in length.