FAQ: Can the NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs) (NEB #E6440, E6442, E6444, and E6446) be used to address “index hopping” with Illumina patterned flow cells?

Yes. The 96 Unique Dual Index Primer Pairs were designed to facilitate sequencing on patterned flow cells for the Illumina instruments where index hopping is problematic. The unique combination of 96 dual indices allows identification and complete filtering of index-swapped reads.

Reference: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4703-0