| Instrument | NextSeq 1000/2000, NovaSeq, any instrument with barcode hopping issues |
|---|---|
| Recommendation | Any of the four NEBNext Multiplex Oligos for Illumina (Unique Dual Index Primer Pairs) Sets 1-4: E6440, E6442, E6444, E6446. |
| <96 samples | Purchase the S size |
| ≥96 samples | Recommendation depends on how many samples user plans on pooling for each sequencing run: |
| If pooling > 96 samples for a single run, users would need multiple UDI Sets. This is more likely with high throughput instruments e.g. NovaSeq. | |
| If ≥96 samples will not be pooled together for a single run, recommend L size of one kit. | |
| Instrument | MiSeq and NextSeq 500/550 |
| Recommendation | Any NEBNext Oligos product can be used. |
| If there is any chance that the libraries will be sequenced on NextSeq or NovaSeq, Unique Dual Index sets are recommended. | |
| <96 samples | If only MiSeqs are available and <96 samples are pooled, the plated 96 single-index primer set (E6609) is the most user-friendly. |
| ≥96 samples | All NEBNext Oligos can be used, and users should decide on their preferred product format. |
| Instrument | MiniSeq |
| Recommendation | Any NEBNext Oligos product can be used. |
| If there is any chance that the libraries will be sequenced on NextSeq or NovaSeq, Unique Dual Index sets are recommended. | |
| <96 samples | If only MiniSeqs are available and <96 samples are pooled, the plated 96 single-index primer set (E6609) is the most user-friendly. |
| ≥96 samples | All NEBNext Oligos can be used, and users should decide on their preferred product format. |
