When clustering Nextera Rapid Capture Enrichment libraries on the cBot and sequencing on the HiSeq 1000/2000, GAIIx, or in High Output mode on the HiSeq 1500/2500, new primers are required whether performing a non-indexed, single-indexed, or dual-indexed run. Use the TruSeq Dual Index Sequencing Primer Box for Paired End runs (catalog # PE-121-1003), which is good for a single run and contains the required primers for sequencing (HP10, HP11, HP12).
Sequencing libraries prepared with the Nextera Rapid Capture Enrichment kits on the MiSeq, NextSeq 500, or HiSeq 1500/2500 rapid run reagent kits does not require any additional sequencing primers. These primers are included in the MiSeq Reagent Kit, NextSeq 500 Kit, and HiSeq 1500/2500 rapid run reagent kits.
Quantifying a Nextera Rapid Capture Enrichment post-enriched library using a fluorometric method results in the following cluster densities. Results can vary based on your method of quantification.
Instrument |
Mode/Version |
Required Concentration (pM) |
Expected Cluster Density (mm2) |
MiSeq
|
v2* |
8–12 |
800,000–900,000 |
v3 |
7–14 |
1,200,000–1,400,000 |
|
NextSeq |
High-output Flowcell |
3 |
200,000–240,000 |
Mid-output Flowcell |
3 |
200,000–240,000 |
|
HiSeq |
High Output |
8-12 |
750,000–950,000 |
Rapid Run |
8-12 |
750,000–950,000 |
|
* Used for Nextera Rapid Capture Custom Enrichment only |
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For more information, see the Illumina Version Compatibility Reference.