Next Generation Genome Sequencers Compared

Desktop sequencers promise to democratize genomics, but it is difficult for researchers who are not experts in sequencing technology to sort through the overheated marketing claims made in this fiercely competitive industry. A group of UK-based researchers therefore decided to put the three leading models — Roche’s 454 GS Junior, Illumina’s MiSeq and Life Technologies’ Ion Torrent Personal Genome Machine (PGM) — through their paces. The test was to sequence the genome of the bacterium Escherichia coli, which killed more than 40 people in Germany last summer.

Nature spoke to Nicholas Loman, a bioinformatician at the University of Birmingham, UK, and one of the authors of the study, asking him what the work reveals about the state of genetic microbial diagnostics. The results are published today in Nature Biotechnology1.
So who won?

Each platform has strengths and weaknesses. If you want the most throughout per hour, the Ion Torrent PGM does that. If you need the highest throughput per run, the MiSeq is there. Accuracy-wise, the MiSeq is best; for generating the longest reads, the 454 is best. Both the PGM and 454 have some problems with accuracy concerning homopolymers [stretches of repeating bases]. And, of course, a user is going to want to look at cost. Part of the point of our paper is that genome sequencing is not a one-size-fits-all solution.
Why did you do this analysis?

As next-generation genome sequencing is going to come into the clinic and into public health, it will be targeted at people who don’t necessarily fully understand these issues. Up until now, people have had to depend on marketing information and blog posts for these comparisons, which are really useful, but can be difficult to find. And the marketing is really quite aggressive, if you remember the Personal Genome Machine vs MiSeq videos that played off the Mac vs PC ads. People are crying out for independent analysis.
Next Generation Genome Sequencers Compared