NovaSeq 6000

Illumina’s NovaSeq 6000 provides you access to the most powerful, high-throughput sequencing instrument available that allows for faster and more cost-effective genomic analyses.

The largest benefit is provided for applications that require large amounts of data, such as human Whole Genome Sequencing (WGS), Exome Sequencing (WES) and tumor–normal profiling. These projects can be analyzed at a sharply reduced price per sample compared to sequencing on all other HiSeq instruments and require only 1 or 2 sequencing days to meet clinical demands.


  • Up to 6 Terabases (Tb) data output per run
  • High quality data (Q30 score >92% in 2018)
  • Lowest price per base
  • Fast run time: 1 or 2 days
  • Scalable

Scalable and Flexible
The NovaSeq 6000 is the first of Illumina’s sequencers that support multiple flow cells that each have a different output range (see table). This gives GenomeScan the opportunity to select the flow cell based on project sizes, thereby selecting the most economical option.

GenomeScan uses three flow cell types, from small to large capacity: S1, S2 and S4. The S2 produces a comparable amount of data as the HiSeq4000, while the S4 produces 3 times more data per run. Recently, the SP flow cell was launched, with enables an fast turn-around time, or projects with aberrant requirements such as mid-read PE250 sequencing. One S4 flow cell generates enough data to analyze >48 full genomes with 30x coverage!

Graph NovaSeq 6000 webpage 1024x607 Illumina NovaSeq 6000: Fast and cost effective genomic analyses

* Human Genomes assumes > 120 Gb of data per sample to achieve 30X genome coverage. Exome assumes ~8Gb/100X. Transcriptomes assume ≥ 50M reads.

To validate the quality of the NovaSeq data-output, GenomeScan has aligned Phage Lambda reads to its reference and observed a staggering percentage perfect reads of 99.2%. This even exceeds the percentage perfect reads of the already very accurate measurements of the HiSeq 4000.

Further reading:

novaseq rendering right Illumina NovaSeq 6000: Fast and cost effective genomic analyses