Chemistry and imaging on the NextSeq 1000/2000

The NextSeq 1000/2000 uses 2-channel chemistry, similar to the NextSeq 500/550, MiniSeq, and NovaSeq 6000. However, instead of using red and green channels, the NextSeq 1000/2000 uses blue and green. Using blue instead of red allows for greater resolution of tightly packed nanowells on the NextSeq 1000/2000 flow cells.

Additionally, the base-dye assignment differs between Standard chemistry and XLEAP chemistry. In particular, the signal assignment for certain bases (notably A and C) is inverted between the two chemistries.

Figure 1: Representation of NextSeq 1000/2000 Standard chemistry dye by nucleotide.

Figure 2: Representation of NextSeq 1000/2000 XLEAP chemistry dye by nucleotide.

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