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: index length is limited by the corresponding BCL Convert limitations. BCL Convert 4.2 or lower is limited to 27 index cycles total. For BCL Convert 4.3 and higher, the index length has been increased to 27 cycles for each index read.

• Local Run Setup:

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

  • Sample Sheet: it is possible to edit the sample sheet manually to set any index length.

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

• The warning will not display if Index 1 or Index 2 is 0 cycles. Note: it is not possible to perform only an Index 2 read; to enable an Index 2 read, an Index 1 read must also be performed.

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 [email protected].