Is there a maximum number of cycles for index reads on the NextSeq 1000/2000?

The maximum number of cycles for an index read is dependent on how run is setup.

• Cloud Setup in BaseSpace Instrument Run Setup: maximum of 10 cycles per index reads.

• Local Run Setup:

  • Standalone: there is no maximum index read length within NextSeq 1000/2000 Control Software.

  • Sample Sheet: it is possible to edit sample sheet manually to run longer than 10 bp within index reads.

NextSeq 1000/2000 Control Software will display a warning when Index 1 and Index 2 are fewer than 6 cycles.

• The warning will not be shown if Index 1 or Index 2 is 0 cycles.

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 #3459), contact Illumina Technical Support [e-mail].