The long reads ahead: de novo genome assembly using the MinION [version 2; referees: 2 approved]

• Main Authors: Carlos de Lannoy, Dick de Ridder, Judith Risse
• Format: Article
• Language: English
• Published: F1000 Research Ltd 2017-12-01
• Series: F1000Research
• Subjects: Bioinformatics; Genomics
• Online Access: https://f1000research.com/articles/6-1083/v2

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 novo sequencing 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has also lead to a lack of overview of the expanding landscape of analysis tools, as performance evaluations are outdated quickly.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.