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Run time estimates for each sequencing step on Illumina sequencing platforms

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 Board Cluster Generation
Cycle Time (Minutes)
Template Building *
Paired End Turnaround
Post-Run Wash / Maintenance Wash
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
75 minutes
MiSeq v2 Chemistry
N/A
60 minutes
Nano = 2.5 Micro = 3 Full = 4.5
Run Continued
31 minutes
Post-Run = 20 minutes Post w/ Template = 30 minutes Maintenance Wash = 90 minutes
MiSeq v3 Chemistry
N/A
70 minutes
6
Run Continued
50 minutes
Post-Run = 20 minutes Post w/ Template = 30 minutes Maintenance Wash = 90 minutes
NextSeq 500/550
N/A
2.5 hr
4.6
Run Continued
60 minutes
90 Minutes
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 Rapid Run v2
N/A
1.5 hr
7
1.5-2 hr
1 hr
Water Wash = 15 minutes Maintenance Wash = 90 minutes
HiSeq 2500 Rapid Run v2 (cBot)
1 hr
1.5 hr
7
1.5-2 hr
1 hr
Water Wash = 15 minutes Maintenance Wash = 90 minutes
HiSeq 2500 TruSeq v3
5 hr
N/A
Single side = 53 Dual side = 67
4-8 hr
4.5 hr
20 (wash only position 1-8) or 60 / 130
HiSeq 2500 TruSeq v4
2 hr
N/A
Single side = 19 Dual side = 30
5-6 hr
3 hr
20 (wash only position 1-8) or 60 / 130
HiSeq 3000/4000
Single Read - 4 hr Paired-End - 3 hr
N/A
Single side = 12 # Dual side = 16 #
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 6000
N/A
130 minutes¤
SP/S1 = 3.5 S2 = 5 S4 = 6.75
N/A
48 minutes
Post-run = 80 minutes Maintenance wash = 80 minutes
NovaSeq X/X Plus
N/A
4.6 hr
B10 = 2.8
N/A
50 minutes
Post-Run = 110 minutes Maintenance = 180 minutes
Instrument
cBot Cluster Generation
On Board Cluster Generation
Cycle Time (Minutes)
Template Building *
Paired End Turnaround
Post-Run Wash / Maintenance Wash
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
75 minutes
MiSeq v2 Chemistry
N/A
60 minutes
Nano = 2.5 Micro = 3 Full = 4.5
Run Continued
31 minutes
Post-Run = 20 minutes Post w/ Template = 30 minutes Maintenance Wash = 90 minutes
MiSeq v3 Chemistry
N/A
70 minutes
6
Run Continued
50 minutes
Post-Run = 20 minutes Post w/ Template = 30 minutes Maintenance Wash = 90 minutes
NextSeq 500/550
N/A
2.5 hr
4.6
Run Continued
60 minutes
90 Minutes
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 Rapid Run v2
N/A
1.5 hr
7
1.5-2 hr
1 hr
Water Wash = 15 minutes Maintenance Wash = 90 minutes
HiSeq 2500 Rapid Run v2 (cBot)
1 hr
1.5 hr
7
1.5-2 hr
1 hr
Water Wash = 15 minutes Maintenance Wash = 90 minutes
HiSeq 2500 TruSeq v3
5 hr
N/A
Single side = 53 Dual side = 67
4-8 hr
4.5 hr
20 (wash only position 1-8) or 60 / 130
HiSeq 2500 TruSeq v4
2 hr
N/A
Single side = 19 Dual side = 30
5-6 hr
3 hr
20 (wash only position 1-8) or 60 / 130
HiSeq 3000/4000
Single Read - 4 hr Paired-End - 3 hr
N/A
Single side = 12 # Dual side = 16 #
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 6000
N/A
130 minutes¤
SP/S1 = 3.5 S2 = 5 S4 = 6.75
N/A
48 minutes
Post-run = 80 minutes Maintenance wash = 80 minutes
NovaSeq X/X Plus
N/A
4.6 hr
B10 = 2.8
N/A
50 minutes
Post-Run = 110 minutes Maintenance = 180 minutes
Table 1. Approximate times for each sequencing step per instrument and supported chemistry
* 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.
For any feedback or questions regarding this article (Illumina Knowledge Article #1540), contact Illumina Technical Support [email protected].
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