Robust long-read native DNA sequencing using the ONT CsgG Nanopore system

The ability to obtain long read lengths during DNA sequencing has several potentially important practical applications. Especially long read lengths have been reported using the Nanopore sequencing method currently commercially available from Oxford Nanopore Technologies (ONT). However, early reports have demonstrated only limited levels of combined throughput and sequence accuracy. Recently, ONT released a CsgG protein-pore based sequencing array as well as a 250b/s pore translocation chemistry with potential for improvements. Here we report the use of such components to obtain long-read data from a native human genome obtained from the near-haploid cancer cell line HAP1. We performed a single sequencing run on ONTs miniature ‘minION’ device from which we were able to obtain ~247,000 high-quality sequence reads, comprising a total of ~2.4 billion bases, with a mean read length of 9.6kb and an N50 of ~17kb. 97% of such reads successfully mapped to reference with a mean identity of 84%. With improved sequencing chemistries already more recently released and higher-throughput instruments in the pipeline, this early study suggests that ONT CsgG-based sequencing may be a useful option for potential practical long-read applications.