Fig. 1 Illustration of a typical approach to genome assembly
Nanopore reads can reach hundreds of kilobases in length, which is more than sufficient to span entire viral genomes in single reads. In contrast, to obtain a complete genome sequence from bacterial, or larger, genomes it is currently necessary to reconstruct the sequence by aligning and joining together overlapping sequence reads. This process is termed ‘de novo genome assembly’ (Fig. 1). Assembling genomes using data from short-read sequencing technologies presents a computational challenge, and the results tend to be imperfect, particularly when the genomes contain extensive repetitive regions. Long reads make assembly far easier, and allow us to resolve repeats and structural variants that are several kilobases in length.