A sequencer coming of age: De novo genome assembly using MinION reads.

Carlos De Lannoy,Dick De Ridder,Judith Risse

doi:10.12688/f1000research.12012.1

Carlos De Lannoy, Dick De Ridder + Show 1 more

Open Access

https://doi.org/10.12688/f1000research.12012.1

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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 novosequencing 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has also lead to a lack of oversight in the expanding landscape of analysis tools, as performance evaluations are outdated quickly. Now that the MinION is approaching a state of maturity, a thorough comparative benchmarking effort of de novoassembly pipelines may be at place. 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
Recent years saw the dawn of what can be perceived as a third generation; one that allows amplification-free reading of single DNA molecules in long consecutive stretches [van Dijk et al, 20141, review.] Currently, this new generation is dominated by two methods: nanopore sequencing and single-molecule real time (SMRT) sequencing, championed by Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), respectively
Since the introduction of the first commercially available nanopore sequencing device, ONT’s MinION, and the start of the MinION Access program (MAP) in 2014, the field of nanopore sequencing has been advancing at a rapid pace; both new applications and improvements to existing ones are published on a regular basis

Summary

12 Dec 2017 version 1

Eccles , Malaghan Institute of Medical Research, Wellington, New Zealand. Henkel , Leiden University, Leiden, The Netherlands Norwegian University of Life Sciences, Oslo, Norway Michael Liem, Leiden University, Leiden, The Netherlands. This article is included in the Nanopore Analysis gateway. Any reports and responses or comments on the article can be found at the end of the article

Introduction

Discussion

37. Baum LE

Findings

45. Zimin A