Recommendations for using custom primers on the NextSeq 500/550

This article provides an overview of Custom Primer Use for the NextSeq500/550. For complete Custom Primer guidance, please review the NextSeq 500 and NextSeq 550 Sequencing Systems Custom Primers Guide.

• Custom primer positions in the reagent cartridge:

  • Custom Read 1 primer: position 7

  • Custom Read 2 primer: position 8

  • Custom Index 1/2 primers: position 9

• Can only one custom index primer be used?

  • With NextSeq Control Software (NCS) v4.0+, one or both custom index primers can be used. For example, the following setups are possible: - Custom i7 only - Custom i5 only - Both custom i7 and custom i5

• Are there rules to using custom primers on the NextSeq 500/550?

  • Rules will be dependent upon the construction of the library.

  • For example, using a custom Read 1 primer assumes a custom P5 adapter, which might also require a custom i5 index primer. However, depending on the library design, this might not be true.

  

Note: Using a custom primer for Index 2 Read is not supported with other combinations or NCS versions earlier than v1.4.

For any feedback or questions regarding this article (Illumina Knowledge Article #2063), contact Illumina Technical Support [e-mail].