Maximum number of cycles for index reads on the NovaSeq X Series

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 10bp per index read for Local run setup and analysis (LOLA) using UI instead of a sample sheet

• 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)

Control Software v1.3:

• Maximum of 26 bp per index when running DRAGEN BCL Convert v4.3.13 and up.

Note: When analyzing a run with BCL Convert v4.1.23 and below, the maximum combined index length (i5 + i7) cannot exceed 27bp 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.

This was updated to 26 bp per Index with DRAGEN BCL Convert v4.3.13 and above.

Note 2: The index length is not limited for runs set up in manual mode without sample sheet. Only limitation is the maximum number of cycles available in the kit used.

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].