The arms race of sequencing has always been about throughput. The big players (Illumina and Life Tech technologies) have engaged in a continual game of one-upmanship over the last few years. As a result, we’ve seen yields skyrocket to from 10 gigabases per run to the current and outrageous 180-200 gb on the HiSeq. Good news for the sequencing centers, if not for their hapless bioinformaticians.

Now the focus seems to be shifting. Not every lab can afford a half-million-dollar instrument. Those that can likely have already bought them, which means that to make another sale, vendors must promise more than just marginal throughput gains. Last year at AGBT, we saw a new company enter the market with the equivalent of a surprise lob. Small-ball, if you will. IonTorrent promised a benchtop sequencer with short run times and appreciable read lengths (100bp) for under $50K.

The strategy was obvious: bring sequencing to the masses at a price most labs could afford. We’re talking about a completely different market here with almost no penetration: single investigators, small labs, even university departments. A new battleground for sequencing.

And in the year that followed, three companies made a play. Roche/454 launched the GS Junior, which is just adorable. Life Technologies acquired IonTorrent. And the current hegemon, Illumina, promised a small-scale version of their flagship sequencing platform: the MiSeq Personal Sequencing System.

Vendor:	IonTorrent (Life)	454 (Roche)	Illumina
Platform:	PGM	GS Junior	MiSeq
Technology:	Semiconductor sequencing	Pyrosequencing	Sequencing-by-synthesis
Read Length:	100 bp	400 bp	1×35 bp 2×100 bp 2×150 bp
Run Time:	1-2 hours	10 hours	4 hours 19 hours 27 hours
Output:	10 mbp	35 mbp	120 mbp 680 mbp 1 gbp

The specs I’ve compiled above are from the company web sites and brochures. The new instruments seem to share a theme: smaller footprints, lower price tags, and run times lasting less than a day. While not suitable for whole-genome or even whole-exome sequencing, these platforms have dozens of other applications: microbial genomes, BACs or cDNAs, targeted (PCR) validation of mutations or structural validation. Heck, it should even be possible to merge the output of these sequencers with whole-genome or exome BAM files.

One thing is clear: this trend will quickly put next-generation sequencing into the hands of just about every investigator who’d like one. And I find that very exciting.

References
Zhao J, & Grant SF (2010). Advances in Whole Genome Sequencing Technology. Current pharmaceutical biotechnology PMID: 21050163