The MiSeq i100 Is 2 Color
We’ve been speculating on the ASeq Discord about the MiSeq i100 chemistry. Specifically wither it’s a 1 or 2 color system.
The iSeq uses a one color chemistry. That is to say, they only use a single excitation and detection wavelength.
As there’s no easy way to read out 4 different bases with a single signal they need to perform the chemistry in two steps:
That’s unlike any of Illumina’s other instruments, all of which either use 4 colors (one for each base) or a 2 color encoding. My default assumption was that the MiSeq i100 uses 1 color too, but turns out that was wrong! As helpfully noted by Anthony Beckhouse (of Illumina):
Below I go into all the technical details, but you can just scroll down to the summary to get a general sense of what this means for Illumina!