Assessing the performance of the Oxford Nanopore Technologies MinION

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 2 kb and 1 kb respectively, while the longest single read was 98 kb. The whole length of a 5 kb 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.

HAsh-MaP-ERadicator: Filtering non-target sequences from next generation sequencing reads

“…This tool was specifically designed with long reads in mind, in particular those possible from the minION in which SNPs far outnumber indels [3] and has previously been shown to produce unidentifiable reads of unknown origin [10]. Future directions include modifications to the underlying data structures to more readily handle indels.…”

“…Emerging technologies promise to push beyond current limitations of read length, albeit at a cost; longer-read technologies presently have been found to have higher error rates [3]. Regardless of the technology used, contamination remains an issue.…”

High Throughput Sequencing: An Overview of Sequencing Chemistry

“…Instead of collecting samples and sequencing them in lab, the sequencers will be taken to field and sequencing will be done in field directly [15,37,38]. However with the current error rate of 38.2 % it needs more improvement on this front [39].…”

Séquençage de l’ADN par nanopores

“…Des protocoles ont été développés pour augmenter la reproductibilité de ces mesures [32]. Des comparaisons avec les autres techniques de séquençage couramment utilisées ont pu montrer que cette méthode est aujourd'hui compétitive pour le séquençage de novo et l'analyse de variants [17,18,33,34]. Aujourd'hui, les recherches académiques et industrielles cherchent à étendre le principe de séquençage par nanopore à d'autres biomolé-cules, en particulier aux polypeptides [35].…”