Performance Specifications

Approximate Run Duration

The duration of a sequencing run depends on read length and version of instrument control software.

Read Length

HCS v2.0 and later with Flow Cell v3

HCS v2.0 and later with Rapid Flow Cell

2 x 101 Cycles

Approx. 10 days

Approx. 27 Hours

2 x 51 Cycles

Approx. 5 days

Approx. 16 Hours

 

System Performance

High Output Run Mode*Rapid Run Mode*
Read Length Dual Flow Cell
(HiSeq 2500 only)
Single Flow Cell
(HiSeq 1500 or 2500)
Dual Flow Cell Run Time Dual Flow Cell
(HiSeq 2500 only)
Single Flow Cell
(HiSeq 1500 or 2500)
Dual Flow Cell Run Time
1 x 36 95-105 Gb 47-52 Gb 2 days 18-22 Gb 9-11 Gb 7 hr
2 × 50 270-300 Gb 135-150 Gb 5.5 days 50-60 Gb 25-30 Gb 16 hr
2 x 100 540-600 Gb 270-300 Gb 11 days 100-120 Gb 50-60 Gb 27 hr
2 x 150 N/A N/A N/A 150-180 Gb 75-90 Gb 40 hr
Reads Passing Filter
Up to 3 billion single reads or 6 billion paired-end reads Up to 1.5 billion single reads or 3 billion paired-end reads Up to 600 million single reads or 1.2 billion paired-end reads Up to 300 million single reads or 600 million paired-end reads
Quality Greater than 85% of bases above Q30 at 2 × 50 bp
Greater than 80% of bases above Q30 at 2 × 100 bp
Greater than 85% of bases above Q30 at 2 × 50 bp
Greater than 80% of bases above Q30 at 2 × 100 bp
Greater than 75% of bases above Q30 at 2 × 150 bp

*Install specifications based on Illumina PhiX control library at supported cluster densities (between 610-678 K clusters/mm2 passing filter using TruSeq v3 Kits or 700-820 clusters/mm2 passing filter using TruSeq Rapid Kits. Run times for rapid run mode correspond to on-board cluster generation (1.5 hr) and sequencing; for high output mode, run times correspond to sequencing only. Performance may vary based on sample quality, cluster density, and other experimental factors. Early HiSeq 2000 instruments will run slightly slower when upgraded to a HiSeq 2500.

Quality Scores

Read Length

Bases Higher than Q30

2 x 101 Cycles

80%

2 x 51 Cycles

85%

A quality score (Q-score) is a prediction of the probability of an error in base calling.

Q-Score

Chance of Wrong Base Call

Q40

1 error in 10,000

Q30

1 error in 1,000

Q20

1 error in 100

Q10

1 error in 10