|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.
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.
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.