Wednesday, 25 April 2012

MiSeq vs PGM Ion Torrent vs 454 GS Junior. And the winner is...

On April 22 the prestigious journal Nature Biotechnologies published the paper Performance comparison of benchtop high-throughput sequencing platforms. The study has been performed by a group of UK-based researchers who decided to sequence with the 3 platforms the genome of the bacterium Escherichia coli, which killed more than 40 people in Germany last summer. Who is the winner. Citing a Nature editorial  by Erika Check Hayden "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". As potential future user of the Ion Torrent PGM we are concerned about the higher error rates of this technology. This is obviously a key factor in the choice of a NGS platform, particularly when researchers are focused on target sequencing of amplicons for the identification of germ line and somatic mutations. Now Life Technologies has to quickly provide detailed information on how the new chemistries and software releases are improving error rates and demonstrate that the levels of accuracy achieved are more than satisfactory also for sequence variation analysis.

By the way, this is the 100th post on this blog!

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