Nick Loman at Pathogens: Genes and Genomes says that the key players emerging third-generation sequencing market are comparable to the Intel x86 family and its famed competitor, reduced instruction set computing — or RISC — chips in the early 1990s. "Despite the seeming obvious killer advantages … RISC chips resoundingly failed in the desktop PC market, never challenging Intel’s dominance," Loman recalls. He writes that labs considering which third-gen sequencing instruments to invest in is "very similar to the common nerd dilemma: buy a new laptop now, or wait for the next model?" Loman wonders whether the theory behind Moore's law will hold true for the transition from second- to third-generation sequencing technologies. "I propose that Illumina are Intel, and the Genetic Analyzer family — GA1, GA II, GAIIx, HiSeq 2000 — are x86. Life Tech is AMD, producing similar technology with much reduced market share," Loman writes, adding that "the third-generation technologies could end up repeating the RISC story."
Continuing the analogy, Loman notes that when RISC was introduced, "there was a huge base of proprietary applications available that only ran on Intel x86 architecture," much like today, where "both the academic community and the commercial companies have invested in the second-generation space," and many have obtained de novo assemblers and aligners specifically for Illumina-generated data. "Finally, Intel managed to outmaneuver the threat from RISC by copying some of the best ideas from RISC and integrating them into the x86 family," Loman writes, evoking the possibility that Illumina could perform a "bolt-on upgrade" to the HiSeq using technologies from Oxford Nanopore, given the January 2009 marketing agreement between the firms. The blogger also says that Helicos BioSciences has "had a torrid time, failing to get any kind of market penetrance" with its single-molecule sequencer. Loman's best guess? "Certain third-generation technologies will be successful but not in direct competition with Illumina," he writes.