Can PhiX be sequenced on the iSeq 100 when using custom primers?

With the release of iSeq Control Software version 3.0, it is now possible to use custom sequencing primers on the iSeq 100. Due to the construction of the iSeq 100 cartridge, it is not possible to spike custom primers directly into the pre-loaded Illumina primers.

In lieu of spiking custom primers directly into reagent cartridge wells, the NextSeq 1000/2000 custom primer kit configurations are compatible with the iSeq 100 and can be used. With this, custom primers can be mixed with Illumina primers and then loaded as a pool into the reagent cartridge as a custom primer for each read.

Refer to the NextSeq 1000/2000 Custom Primer Kit Configurations for available kit configurations and their part numbers.

iSeq 100 specific guidance for adding custom primers:

Kit version	Illumina Primer (name)	Cartridge Position	Total volume (µL)	Custom primer final concentration (µM)
	Read 1 (HP21)	NA	140	0.3
i1 v2	Index 1 (i7) (BP14)	NA	140	0.6
	Index 2 (i5) (BP14)	NA	140	0.6
	Read 2 (HP21)	NA	140	0.3

For further information, search for Knowledge Base article Spiking custom primers into the Illumina sequencing primers.

For any feedback or questions regarding this article (Illumina Knowledge Article #6502), contact Illumina Technical Support [e-mail].