Blog:Explanation of the difference between 2- and 4-channel sequencing by Illumina

Question

[Adele Feuerstein]

The four-dye system, with four distinct ‘colors’ for calling the DNA bases, is the standard for Illumina technology. But lately Illumina changed it. For the new machines, like MiniSeq, NextSeq and NovaSeq, Illumina uses an alternative system with just two dyes. How is it possible to detect four different bases on that system?

We explain it on our website.

[GenoMax]

Illumina 2-channel technology spotlight note. Direct from Illumina.

[Joe]

EDIT - realised this isnt a question... d'oh

[WouterDeCoster]

If I'm not mistaken the novaseq will also use two-dye chemistry.

[David Langenberger]

Also HiSeq X Five/Ten.

[GenoMax]

Are you sure? I don't have first hand experience with X5/10 but I think they still use 4 color chemistry.

Apparently at AGBT the buzz was (only have second-, third-hand information) that Illumina was going to move to 2 color chemistry for all future sequencers.

[David Langenberger]

You're right. I was thinking of the patterned flow cells. That was new in the X10.

Answer 1

[Lars]

Thank you for this nice summary. My first experiences with the miniSeq were not good. Quality of the reads was bad. Perhaps it was because of the 2-channel chemistry. Now it seems better.