Assessing the performance of the Oxford Nanopore Technologies MinION

T Laver,J Harrison,P.A O’Neill,K Moore,A Farbos,K Paszkiewicz,D.J Studholme

doi:10.1016/j.bdq.2015.02.001

T Laver, J Harrison + Show 5 more

Open Access

https://doi.org/10.1016/j.bdq.2015.02.001

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Abstract

The Oxford Nanopore Technologies (ONT) MinION is a new sequencing technology that potentially offers read lengths of tens of kilobases (kb) limited only by the length of DNA molecules presented to it. The device has a low capital cost, is by far the most portable DNA sequencer available, and can produce data in real-time. It has numerous prospective applications including improving genome sequence assemblies and resolution of repeat-rich regions. Before such a technology is widely adopted, it is important to assess its performance and limitations in respect of throughput and accuracy. In this study we assessed the performance of the MinION by re-sequencing three bacterial genomes, with very different nucleotide compositions ranging from 28.6% to 70.7%; the high G+C strain was underrepresented in the sequencing reads. We estimate the error rate of the MinION (after base calling) to be 38.2%. Mean and median read lengths were 2kb and 1kb respectively, while the longest single read was 98kb. The whole length of a 5kb rRNA operon was covered by a single read. As the first nanopore-based single molecule sequencer available to researchers, the MinION is an exciting prospect; however, the current error rate limits its ability to compete with existing sequencing technologies, though we do show that MinION sequence reads can enhance contiguity of de novo assembly when used in conjunction with Illumina MiSeq data.

Highlights

The Oxford Nanopore Technologies (ONT) MinION [20] is a new sequencing technology that is currently available as part of an early access and development scheme: the MinION Access Programme [21]
To investigate a potential bias against extreme G + C sequences we split the E. coli and B. burgdorferi genomes into 1000 bp windows using BEDTools [25] using the LAST alignment of the MinION reads against the reference genome sequences we evaluated the coverage depth of the alignment for those windows using BEDTools
Our results demonstrate that in spite of its high error rate the MinION is able to generate extremely long reads, is able to span regions of interest in a single read and is able to improve the contiguity of genome assemblies

Summary

Introduction

The Oxford Nanopore Technologies (ONT) MinION [20] is a new sequencing technology that is currently available as part of an early access and development scheme: the MinION Access Programme [21]. This programme allowed early access to the MinION for participating sequencing centres. Laszlo et al [13] sequenced the phi X 174 genome using another nanopore based technology, demonstrating that nanopore sequencing can produce long reads that are accurate enough to enable them to be aligned back to their reference genomes

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