12/10/2022
The run time specifications for Illumina sequencing runs include cluster generation, SBS chemistry cycles, paired-end chemistry, and wash steps. In addition, runs that use non-patterned flow cells pause for a template building step. To aid in planning sequencing workflows and in estimating overall run times, Table 1 summarizes the estimated length of each sequencing step for Illumina sequencing platforms and chemistry versions.
| Instrument | cBot Cluster Generation |
On Instrument Cluster Generation |
Cycle Time (Minutes) |
Template Building** |
Pair End Turnaround |
Quick Wash/Manual or Maintenance Wash (Minutes) |
|---|---|---|---|---|---|---|
| iSeq 100 | N/A | 5 hr | 2.2 | N/A | 52 Minutes | No wash |
| MiniSeq | N/A | 90 Minutes | 3.5 | Run continued | 60 Minutes | 20 / 75 |
| MiSeq v2 | N/A | 60 Minutes | 4.5 (Micro = 3 and Nano = 2.5) |
Run continued | 31 Minutes | 20 (30 w/ Template Line) / 90 |
| MiSeq v3 | N/A | 70 Minutes | 6 | Run continued | 50 Minutes | 20 (30 w/ Template Line) / 90 |
| NextSeq 500/550 | N/A | 2.5 hr | 4.6 | Run continued | 60 Minutes | 20 / 90 |
| NextSeq 1000/2000 P1 | N/A | 3.75 hr | 2.5 | N/A | 40 Minutes | Optional Purge: 1.5 hr |
| NextSeq 1000/2000 P2 | N/A | 4 hr | 3.5 | N/A | 40 Minutes | Optional Purge: 1.5 hr |
| NextSeq 1000/2000 P3 | N/A | 4 hr | 5 | N/A | 45 Minutes | Optional Purge: 3 hr |
| HiSeq 2500 RRv2 OBCG* |
N/A | 1.5 hr | 7 | 1.5 - 2 hr | 1 hr | 15 / 60 |
| HiSeq 2500 RRv2 w/ cBot |
1 hr (Template delivery only) |
1.5 hr | 7 | 1.5 - 2 hr | 1 hr | 15 / 60 |
| HiSeq 2500 TruSeq v3 |
< 5 hr | N/A | 53 67 (if running both FC) |
4 - 8 hr | 4.5 hr | 20 (wash only position 1-8) or 60 / 130 |
| HiSeq 2500 HiSeq v4 |
2 hr | N/A | 19 30 (if running both FC) |
5 - 6 hr | 3 hr | 20 (wash only position 1-8) or 60 / 130 |
| HiSeq 3000/4000 |
3 hr - Paired End 4 hr - Single Read |
N/A | 12# 16# (if running both FC) |
N/A | 2.5 hr | 20 (wash only position 1-8) or 60 / 130 |
| HiSeq X v2.5 | 3 hr | N/A | 12# | N/A | 2.5 hr | 20 (wash only position 1-8) or 60 / 130 |
| NovaSeq | N/A | 130¤ Minutes | SP/S1 = 3.5 S2 = 5 S4 = 6.75 |
N/A | 48 Minutes | 80 |
Table 1. Approximate times for each sequencing step per instrument and supported chemistry
* OBCG = On-Board Cluster Generation
** Template building time will vary based on cluster density
¤ XP workflow is approximately 115 minutes as ExAmp step is skipped
# Cycles 2-5 on these runs can take up to 25 minutes each
Estimated run times will depend on cluster density and available computer resources. If the hard drive does not have sufficient space for data processing, or network location speeds are slow, run times may be prolonged. Total run times for the maximum read lengths of Illumina platforms, and other sequencing run specifications, can be found on the Illumina Sequencing Platforms web page.