NovaSeq6000 - Index hopping

The Novaseq is a 2-color technology that produces high quality data: https://www.illumina.com/content/dam/illumina-marketing/documents/products/appnotes/novaseq-hiseq-q30-app-note-770-2017-010.pdf.

It should be noted that Novaseq is a patterned flow cell technology that has an increased rate of index hopping, which is most likely library dependent.

Typical levels of index hopping on patterned flow cell systems range from 0.1–2% depending on the type, quality, and handling of the library. Use of unique dual indexing eliminates hopped reads from downstream analysis because unexpected combinations will be assigned as undetermined.

See more info in:

https://emea.illumina.com/science/education/minimizing-index-hopping.html

https://www.illumina.com/content/dam/illumina-marketing/documents/products/whitepapers/index-hopping-white-paper-770-2017-004.pdf