Hybrid Nanopore and Illumina Genome Assembly

A DNA library for MinION sequencing was prepared based on the protocol for the Rapid Lambda Control Experiment using the Rapid Sequencing Kit (Oxford Nanopore Technologies). The library was loaded onto MinION R9.5 SpotON Flow Cells (Oxford Nanopore Technologies). Base calling was performed by MinKnow. Genome assembly was conducted using Canu v1.6 with the parameter “-nanpore-raw”. The assembled contigs were corrected using short reads obtained from the linked-read library using the HiSeq X platform. The paired-end reads were mapped to the assembled sequences by BWA-0.7.15 with the parameters “mem -M -T 30” (Li and Durbin 2009 (link)). Processing was performed using samtools-1.4 with the steps “view -q 30 -F 0x100” and “view -f 0x2” (Li 2011 (link)). Finally, polymorphisms detected by the Genome Analysis Toolkit HaplotypeCaller with the options “-out_mode EMIT_VARIANTS_ONLY–variant_index_type LINEAR–variant_index_parameter 128000–filter_reads_with_N_cigar” (McKenna et al. 2010 (link)) were incorporated into the assembled sequences using bcftools-1.4 with the option “consensus” (Li 2011 (link)).