Abstract
Nanopore technology provides a novel approach to DNA sequencing that yields long, label-free reads of constant quality. The first commercial implementation of this approach, the MinION, has shown promise in various sequencing applications. This review gives an up-to-date overview of the MinION's utility as a de novosequencing device. It is argued that the MinION may allow for portable and affordable de novo sequencing of even complex genomes in the near future, despite the currently error-prone nature of its reads. Through continuous updates to the MinION hardware and the development of new assembly pipelines, both sequencing accuracy and assembly quality have already risen rapidly. However, this fast pace of development has also lead to a lack of overview of the expanding landscape of analysis tools, as performance evaluations are outdated quickly. As the MinION is approaching a state of maturity, its user community would benefit from a thorough comparative benchmarking effort of de novo assembly pipelines in the near future. An earlier version of this article can be found on bioRxiv.
Highlights
The development of novel genome sequencing methods has been a major driving force behind the rapid advancements in genomics of the last decades
In our description of the physical DNA sequencing process, part 1 of our review, minor revisions were made; the R9.5 pore is briefly introduced under “structure and charge of the nanopore”, mock data used in the example of the MinION raw signal in Figure 3 has been replaced by actual data, and the flowcell grid layout cartoon in Figure 5 has been adapted to show more diverse defects that may occur in a well
Recent years saw the dawn of what can be considered a third generation; one that allows amplification-free reading of single DNA molecules in long consecutive stretches[1]. This new generation is dominated by two methods: nanopore sequencing and singlemolecule real time (SMRT) sequencing, championed by Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), respectively
Summary
We hereby present a revised version of our review, based on the comments made by the referees and new developments since version 1 was published. In our description of the physical DNA sequencing process, part 1 of our review, minor revisions were made; the R9.5 pore is briefly introduced under “structure and charge of the nanopore”, mock data used in the example of the MinION raw signal in Figure 3 has been replaced by actual data, and the flowcell grid layout cartoon in Figure 5 has been adapted to show more diverse defects that may occur in a well. The text on Metrichor basecallers has been revised and the descriptions of older basecallers, Nanocall and DeepNano, have been omitted, while two newer tools, Chiron and BasecRAWller, have been added. We thank all involved referees for their thorough assessments, which we believe have helped us to improve the manuscript
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