1. First-, second-, and third-generation sequencing platforms are currently available, and each has distinct advantages and disadvantages.
First-, second-, and third-generation sequencing platforms are currently available, and each has distinct advantages and disadvantages. First-generation sequencers, including the ABI capillary sequencer, are characterized by high accuracy and a relatively long read length; however, these systems are not amenable to high-throughput sequencing. Second-generation platforms include MiSeq, HiSeq, and NextSeq from Illumina, as well as Ion Torrent from Thermo Fisher Scientific. These platforms use massively parallel sequencing to achieve high throughput and have high base-calling accuracy; however, sequencing reads are short and this can result in split contigs in repetitive regions during sequence assembly. Third-generation sequencers, including PacBio from Pacific Biosciences and MinION, PromethION, and SmidgION from Oxford Nanopore Technologies, are able to sequence single-molecule templates, which results in very long read length at a high throughput. Third-generation sequencers have a very high error rate relative to the other technologies. Currently, the optimal sequencing platform is highly dependent on the desired applications.
J. Ronholm et al. Clin. Microbiol. Rev. 2016; doi: /CMR