Specifications

HiSeq System Performance Parameters

High Output Run Mode*
  HiSeq SBS v4 SPECIFICATIONS TruSeq SBS v3
Read length Dual Flow Cell Single Flow Cell Dual Flow Cell Run Time Dual Flow Cell Single Flow Cell Dual Flow Cell Run Time
1×36 128-144 Gb 64-72 Gb 29 hrs 95-105 Gb 47-52 Gb 2 days
2×50 360-400 Gb 180-200 Gb 2.5 days 270-300 Gb 135-150 Gb 5.5 days
2×100 720-800 Gb 360-400 Gb 5 days 540-600 Gb 270-300 Gb 11 days
2×125
900-1 Tb 450-500 Gb 6 days N/A N/A N/A
Reads Passing Filter Up to 4 billion single read or 8 billion paired-end reads Up to 2 billion single read or 4 billion paired-end reads   Up to 3 billion single read or 6 billion paired-end reads Up to 1.5 billion single read or 3 billion 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 80% of bases above Q30 at 2×125 bp
Greater than 85% of bases above Q30 at 2×50 bp
Greater than 80% of bases above Q30 at 2×100 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 870-930 K clusters/mm2 passing filter using HiSeq v4). Run times for high output mode correspond to sequencing only. Performance may vary based on sample quality, cluster density, and other experimental factors.

Rapid Run Mode*
 
Read length Dual Flow Cell Single Flow Cell Dual Flow Cell Run Time
1×36 18-22 Gb 9-11 Gb 7 hr
2×50 50-60 Gb 25-30 Gb 16 hr
2×100 100-120 Gb 50-60 Gb 27 hr
2×150 150-180 Gb 75-90 Gb 40 hr
Reads Passing Filter Up to 600 million single read or 1.2 billion paired-end reads Up to 300 million single read 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 75% of bases above Q30 at 2×150 bp

*Install specifications based on Illumina PhiX control library at supported cluster densities (between 700-820 K 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. 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.