[femto]

I'd make two observations:

1) Illumina/Solexa's breakthrough was to convert sequencing into a problem limited by computing resources (reassembling the jigsaw), so they were able to leverage improvements in semiconductor processing.

2) This quote grabbed me:

"But Flatley is confident that Illumina’s footprint, which includes not just machines but also the software to handle genomic data, will make the company hard to unseat."

A call to arms for the Free Software movement?

[daughart]

As for your first point, shotgun sequencing was not invented by Illumina. Shotgun sequencing, or sequencing many small fragments and then computationally reconstructing a larger contig, was first done in 1979, and later used by many groups (most famously by Celera Genomics in their quest to beat the human genome project). Shotgun sequencing can be done using any short sequencing reads, so this is neither a breakthrough nor even an advantage for Illumina.

Illumina's chemistry was better than the others, and they marketed their advantages better. The Illumina machine produced longer reads than SOLiD (Life Technologies), and produced more reads than 454 (Roche). They produced reliable instruments that were relatively easier to use than the others also, which made them favorites for core facilities.

[diego_moita]

> A call to arms for the Free Software movement?

No chance, these algorithms are too dependent on very expensive hardware that sole coders can't afford.