Finishing the Job - Utility of Long-Read Sequencing Using the Minion for Bacterial Genomics

Abstract

Sequencing technologies have evolved dramatically since the first two bacterial genomes were published. Currently, due to second generation sequencing, millions of bacterial genomic sequences exist, although a significantly smaller amount represent completely assembled genomes. Third generation sequencing allows the analysis of single molecules, with read-lengths that cover highly complex repetitive regions previously inaccessible by short-read sequencing. However, long-read sequencing is known for producing errors which make long-read-only genome assemblies unreliable or complex if high accuracy is important for further applications. Here, Oxford Nanopore Technology's MinION, the first handheld nanopore sequencing device, is evaluated in comparison with competing sequencing platforms. The MinION's applications, potential and limitations are reviewed, focusing on its utility for bacterial genome de novo or hybrid assembly.