Indexing considerations for NextSeq 500/550 sample sheets
Last updated
Was this helpful?
Last updated
Was this helpful?
A sample sheet is only required for offline analysis using bcl2fastq.
Read lengths are entered either in Local Run Manager, in PrepTab (NextSeq Control Software (NCS) v2.2 or lower), or in the Control Software directly if operating in standalone/manual mode.
Select index sequences that contain at least one base other than G for the first two cycles.
If an Index Read begins with two base calls of G only, the cluster registration will fail because there is no signal intensity.
This requirement for index diversity is compatible with any Illumina index selection for single-plex indexing except i7 [H/N]705, which uses the sequence GGACTCCT.
Mixed index lengths are not supported on the NextSeq 500/550.
It is possible to configure different index 1 and 2 lengths in Local Run Manager or Manual Run Mode. - For this, use Manual Run Mode to set up multiple analyses using separate sample sheets in bcl2fastq2.
It is not possible to configure different index 1 and 2 lengths in PrepTab and N-padding is not possible.
The maximum index length is 20 cycles on the NextSeq 500/550.
For further information, search for Knowledge Base article Library pooling guidelines for the NextSeq 500/550 and MiniSeq systems.
For any feedback or questions regarding this article (Illumina Knowledge Article #2129), contact Illumina Technical Support .