2014 NGS Field Guide: Resistance is Futile (mostly, at least for a while)

Alineando secuencias (1)

Photo by Shary.

This year, to introduce the 2014 update to his Next Generation Sequencing Field Guide—perennially our most-accessed community resource—Travis Glenn has a bit more to say than just what goes in the tables. So here it is as a guest post!
Welcome to the 2014 update of the NGS Field Guide. Previously, I have presented the data & left the interpretation of those data to the readers, other than my “grades” about the utility of specific platforms for specific applications (i.e., Tables 1a, 1b, and 1c). However, many of the people that I have corresponded with have asked me to cut to the chase and just make a recommendation. So, by popular demand, in this year’s edition I am being much more direct about my recommendations.
Overall, if you are in the market for a next generation DNA sequencer in early 2014, the data indicate one clear inexorable trend – think Illumina. For fans of the Brady Bunch – Illumina, Illumina, Illumina! For fans of Star Trek – Prepare to be assimilated by one of Illumina’s Borg-like cubes. For fans of Henry Ford – You can have any NSG instrument you want, so long as it’s an Illumina.
OK, it’s not quite that clear-cut, but it isn’t far from it. For the average scientists who just want to get stuff done, then there are few compelling reasons to do anything other than use Illumina sequencers, especially with the introduction of the anti-proton NextSeq 500. The biggest problem with Illumina instruments is that they take a good while to collect all that data and that frequently creates long queues to get samples run (up to months at the lowest-cost high-quality sequencing facilities). The relatively low cost and low maintenance of the Illumina MiSeq and NextSeq 500 are likely to be especially attractive purchases for molecular ecologists who can afford them to avoid the queues.
To be fair to the other companies, there are some situations where it can make sense to purchase and use an Ion Torrent instrument or to use a PacBio. The Ion Torrent PGM and Proton can deliver data significantly faster than any Illumina and the PacBio delivers reads even faster and that are much longer than any other current instrument. Additionally, there is great anticipation for sequencers in development, such as the offerings from Oxford Nanopore, which may have run times and read lengths that could outperform PacBio by quantum leaps. Oxford Nanopore has released sufficient information that some forecasts can be made, but other companies (such as Genia and Genapsys) are developing perhaps even better technologies, but have kept silent about details other than stating their goal of delivering a human genome sequence for $100.
As much as I or anyone else wants to see a good diversity of platforms to help keep the pressure on Illumina so that it doesn’t do an Orwellian Animal Farmesque transformation into ABI or Microsoft, it’s clear that other platforms are currently side shows compared to the Illumina juggernaut. Helicose is gone. Roche has announced an end to support for the 454 platform and it’s only a matter of time until Life Technologies does the same for SOLiD. Illumina’s NextSeq 500 puts a serious dent in the arguments to switch to Ion Torrent.
Until the nanopore or electronic sequencers arrive en mass, Illumina appears set to be the dominant NGS platform. Even after they arrive, Illumina will likely continue to be dominant, then competitive and then co-exist for quite some time. Illumina is currently the big dawg, and if you peruse these tables, you will understand why.

About Jeremy Yoder

Jeremy B. Yoder is an Associate Professor of Biology at California State University Northridge, studying the evolution and coevolution of interacting species, especially mutualists. He is a collaborator with the Joshua Tree Genome Project and the Queer in STEM study of LGBTQ experiences in scientific careers. He has written for the website of Scientific American, the LA Review of Books, the Chronicle of Higher Education, The Awl, and Slate.
This entry was posted in howto, methods, next generation sequencing. Bookmark the permalink.