Can custom primers be used on the NovaSeq 6000 System?

Yes, the NovaSeq 6000 supports the use of custom sequencing primers for Read 1, Read 2, and the Index Reads.

Positions 5, 6, and 7 on the cluster cartridge are reserved for custom primers. The control software includes an option to select custom primers during run setup.

See the NovaSeq Series Custom Primers Guide for additional information.

If spiking custom primers into the Illumina primers, see Knowledge Base articleSpiking custom primers into the Illumina sequencing primers.

For any feedback or questions regarding this article (Illumina Knowledge Article #2571), contact Illumina Technical Support [e-mail].