[Brian Bushnell]

So I took another look at this and it strikes me that the whole problem is the use of only four fluors for 16 combinations. (Seems odd that this wasn't the primary issue attempted to be solved; i.e generating 16 distinct fluors.) Once I got that part, it became obvious why there's an issue with colourspace. Curiously, I just found out that MiniSeq and NextSeq from Illumina use only two fluors - seems like a huge potential issue is one isn't resequencing a human genome...

Yes, if Solid had used 16 colors it might have been substantially better, though that would have added its own unique issues (like potentially taking 4x as long to sequence).

Illumina's 2-color chemistry is not like Solid Colorspace, though. It's just a binary encoding of bases -> colors; no information is lost (since no two bases share the same pair of color polarities), except that you can no longer distinguish between no signal and one of the bases. It works fairly well in practice (for de-novo sequencing) and you don't need to align sequences to determine what they are. The 2-color platforms have weaknesses, but it is not clear that the weaknesses are linked to the number of dyes.