Performance specifications for the HiSeq 2500 System

HiSeq 2500 provides a flexible solution for high-throughput sequencing applications with both High Output and Rapid Run modes

HiSeq 2500 Specifications

Kit Specifications
HiSeq SBS V4
Read length 1 × 36 bp 2 × 50 bp 2 × 100 bp 2 × 125 bp
Dual Flow Cell 128–144 Gb 360–400 Gb 720–800 Gb 900 Gb–1 Tb
Single Flow Cell 64–72 Gb 180–200 Gb 360–400 Gb 450–500 Gb
Dual Flow Cell Run Time 29 hrs 2.5 days 5 days 6 days
TruSeq SBS V3
Read length 1 × 36 bp 2 × 50 bp 2 × 100 bp 2 × 125 bp
Dual Flow Cell 95–105 Gb 270–300 Gb 540–600 Gb N/A
Single Flow Cell 47–52 Gb 135–150 Gb 270–300 Gb N/A
Dual Flow Cell Run Time 2 days 5.5 days 11 days N/A
Additional Kit Specifications
HiSeq SBS V4
Flow Cell Type Dual Flow Cell Single Flow Cell
Reads Passing Filter (8 lanes per flow cell) Up to 4 billion single read or 8 billion paired-end reads Up to 2 billion single read or 4 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
TruSeq SBS V3
Flow Cell Type Dual Flow Cell Single Flow Cell
Reads Passing Filter (8 lanes per flow cell) 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

*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.

Kit Specifications
HiSeq Rapid SBS Kit V2
Read length 1 × 36 bp 2 × 50 bp 2 × 100 bp 2 × 150 bp 2 × 250 bp
Dual Flow Cell 18–22 Gb 50–60 Gb 100–120 Gb 150–180 Gb 250–300 Gb
Single Flow Cell 9–11 Gb 25–30 Gb 50–60 Gb 75–90 Gb 125–150 Gb
Dual Flow Cell Run Time 7 hr 16 hr 27 hr 40 hr 60 hr
Additional Kit Specifications
HiSeq Rapid SBS Kit V2
Flow Cell Type Dual Flow Cell Single Flow Cell
Reads Passing Filter (2 lanes per flow cell) 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 × 250 bp

† Install specifications based on Illumina PhiX control library at supported cluster densities (between 700–820 K clusters/mm2 passing filter using HiSeq Rapid v2 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.

MiSeq FGx System Specification Sheet

HiSeq 2500 System Specification Sheet

Power and efficiency for production-scale sequencing.

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Sequencing by Synthesis (SBS) Technology

The HiSeq 2500 System harnesses proven Illumina SBStechnology to deliver highly accurate data and robust performance for a broad range of applications. SBS uses a reversible-terminator method, with fluorescently labeled nucleotides to detect single bases as they are incorporated into growing DNA strands.

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Paired-End Sequencing Technology

Paired-end sequencing enables both ends of the DNA fragment to be sequenced. Because the distance between each paired read is known, alignment algorithms can use this information to map the reads over repetitive regions more precisely. This results in much better alignment of the reads, especially across difficult-to-sequence, repetitive regions of the genome.

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