HiSeq 3000/HiSeq 4000 System quality and performance

Illumina sequencing by synthesis chemistry and patterned flow cell technology enable high-throughput, cost-effective NGS

HiSeq 3000/HiSeq 4000 Specifications

  HiSeq 3000 System HiSeq 4000 System
No. of Flow Cells per Run 1 1 or 2
Data Yield - 2 × 150 bp 650–750 Gb 1300–1500 Gb
Data Yield - 2 × 75 bp 325–375 Gb 650–750 Gb
Data Yield - 1 × 50 bp 105–125 Gb 210–250 Gb
Clusters Passing Filter (8 lanes per flow cell) up to 2.5B single reads or 5B paired end reads up to 5B single reads or 10B PE reads
Quality Scores - 2 × 50 bp ≥ 85% bases above Q30 ≥ 85% bases above Q30
Quality Scores - 2 × 75 bp ≥ 80% bases above Q30 ≥ 80% bases above Q30
Quality Scores - 2 × 150 bp ≥ 75% bases above Q30 ≥ 75% bases above Q30
Daily Throughput > 200 Gb > 400 Gb
Run Time < 1–3.5 days < 1–3.5 days
Human Genomes per Run* up to 6 up to 12
Exomes per Run up to 48 up to 96
Transcriptomes per Run up to 50 up to 100

Install specifications based on Illumina PhiX control library at supported cluster densities (between 1310–1524 K/mm2 passing filter). Run times correspond to sequencing only. Performance may vary based on sample quality, cluster density, and other experimental factors.
*Assumes >30× coverage of a human genome.
†Assumes 100× coverage with 80% on target using 2 × 75 bp reads.
‡Assumes 50 million reads per sample.

HiSeq X Series Specification Sheet

Evaluate the HiSeq 3000/HiSeq 4000 Systems

Generate up to 1.5 Tb and 5 billion reads per run. Learn more about the HiSeq 3000/HiSeq 4000 Sequencing Systems.

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Sequencing by Synthesis (SBS) Technology

The HiSeq 3000/HiSeq 4000 Systems leverage sequencing by synthesis (SBS) technology, the most widely adopted next-generation sequencing (NGS) technology in the industry, to ensure high data quality. SBS is the same proven technology used by all Illumina sequencing platforms. The technology supports massively parallel sequencing using a proprietary fluorescently labeled reversible terminator method.

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Patterned Flow Cell Technology

The HiSeq 3000/HiSeq 4000 Systems utilize innovative patterned flow cell technology, which offers an exceptional level of throughput for diverse sequencing applications. Patterned flow cells contain billions of nanowells at fixed locations, a design that provides even spacing of sequencing clusters. This delivers significant increases in sequencing reads and total output of the system.

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