Maximum number of cycles for index reads on the NovaSeq X/X Plus

The maximum number of cycles for an index read is dependent on where the run is setup (cloud vs local) and the software version.

Definitions:

LOLA: Local Orchestrated Local Analysis

COCA: Cloud Orchestrated Cloud Analysis

OLA: On-Instrument Local Analysis

Control Software v1.0:

• Maximum of 10bp per index read for local setup and analysis (LOLA)

Control Software v1.1:

• Maximum of 10bp per index read for local setup and local analysis (LOLA)

• Maximum of 12bp per index read for Manual Mode run setup and local analysis (OLA)

• Maximum of 12bp per index read for BaseSpace run setup and analysis (COCA)

Control Software v1.2:

• Maximum of 12bp per index read for all three run setups: Local run setup and analysis (LOLA), manual mode run setup and local analysis (OLA), and BaseSpace run setup and cloud analysis (COCA)

When analyzing a run with BCL Convert, the maximum combined index length (i5 + i7) cannot exceed 26bp due to software limitations.This restriction is for index lengths only (cycles that are denoted with "I"). "N" masking and "U" for UMIs in the index reads cycles are only counted against the total number of cycles supported by the cartridge.

For further information, search for Knowledge Base article Maximum read length for Illumina sequencing platforms support.

For any feedback or questions regarding this article (Illumina Knowledge Article #8417), contact Illumina Technical Support [e-mail].