NovaSeq 6000

NovaSeq 6000 Instrument Image

In 2017, Illumina announced new sequencers, NovaSeq 6000, that could potentially reduces the cost of human genome sequencing to $100 in the future. NovaSeq is assembled with a new set of flowcells: S1, S2, S3, and S4. Both the systems can work with either one or two flow cells. In addition, NovaSeq 6000 can do 2×50 bp, 2×100 bp, and 2×150 bp read length using flow cells S1 and S2, pretty similar to the existing Illumina machines.

The NovaSeq 6000 System unleashes a new era in sequencing with groundbreaking innovations, providing users with the throughput, speed, and flexibility to complete projects faster and more economically than ever before, which are built from the ground up, offers scalability and flexibility for any type of sequencing, either large scale or targeted sequencing.

The NovaSeq Series lets you take your research further with a wide range of projects sizes for diverse applications—all on a single system. This platform redefines high throughput sequencing with unrivaled throughput, ease of use, low per sample costs, and unmatched flexibility. Whether you are interested in higher output applications for larger-scale projects or lower output applications for smaller-scale projects, the NovaSeq Series will empower you with new possibilities. Watch whole-genome and whole-exome sequencing demonstrations and learn how the NovaSeq Series can meet your lab's evolving needs.

Highlights of NovaSeq 6000:

  • Scalable Throughput. The NovaSeq 6000 System offers high-throughput sequencing across a broad range of applications. Meet your research needs with unprecedented throughput at the lowest cost per sample
  • Highly Flexible. Match data output to project needs. With the ability to choose from 4 different flow cell types, the output can be configured to match your application and project. One, or two, independently operated flow cells can be easily loaded into place to fit your evolving needs.
  • Mature technology: The NovaSeq series epitomizes Illumina's powerful, streamlined, and scalable high-throughput sequencing platform, with its cornerstone being the proven Illumina SBS technology. This method, based on reversible terminators, enables the massive parallel sequencing of billions of DNA fragments, detecting them as individual bases are incorporated into growing DNA strands. By reducing the errors caused by nucleotide repeats (homopolymers) and detection misses, this approach ensures robust and accurate sequencing outcomes.
  • A board range of application. High-quality, high-coverage sequencing offers a comprehensive view of the genome to detect variants accurately, characterize isoforms, and more. The NovaSeq 6000 System allows you to adapt the run to meet your study's specific needs. Whether exploring the genome, epigenome, or transcriptome, the possibilities for your research are endless.

NovaSeq 6000 Performance Parameters

Flow cell type SP S1 S2 S4
Lanes per flow cell 2 2 2 2
Output per flow cell
2×50 bp 65-80 Gb 134-167 Gb 333-417 Gb N/A
2×100 bp N/A 266-333 Gb 667-833 Gb 1600-2000 Gb
2×150 bp 200-250 Gb 400-500 Gb 1000-1250 Gb 2400-3000 Gb
Single reads 0.65-0.8 B 1.3-1.6 B 3.3-4.1 B 8-10 B
Paired-end reads 1.3-1.6 B 2.6-3.2 B 6.6-8.2 B 16-20 B
Quality scores
2×50 bp ≥ 85%
2×100 bp ≥ 80%
2×150 bp ≥ 75%
Run time
2×50 bp ~13 hr ~13 hr ~16 hr N/A
2×100 bp N/A ~19 hr ~25 hr ~36 hr
2×150 bp ~25 hr ~25 hr ~36 hr ~44 hr

Workflow of NovaSeq 6000:

The standard operating procedure on the NovaSeq 6000 system encompasses several imperative stages:

  • Library Preparation: Commencing with DNA or RNA specimens, this phase involves fragmenting the genetic material, ligating adapters, and conducting amplification.
  • Cluster Generation: The libraries are introduced to the flow cell, catalyzing the emergence of clonal DNA fragment conglomerates via bridge amplification techniques.
  • Sequencing: The flow cell is integrated into the NovaSeq 6000 system, wherein cutting-edge optics and expedited sequencing chemistries capture the genomic information.
  • Data Analysis: The sequencing output is subjected to analysis utilizing Illumina's suite of bioinformatics resources, facilitating streamlined operations like alignment, variant identification, and subsequent data interpretation.

Applications of NovaSeq 6000:

The NovaSeq 6000 system's adaptability enables a wide range of applications, encompassing:

  • Whole-Genome Sequencing: Comprehensive examination of entire genomes crucial for population genetics, evolutionary biology, and clinical genomics.
  • Exome Sequencing: Focused sequencing of gene exons to pinpoint coding variants linked to diseases.
  • Transcriptome Sequencing (RNA-Seq): Gaining insights into gene expression, uncovering novel transcripts, and probing gene regulation and function.
  • Epigenomics: Delving into epigenetic alterations like DNA methylation and histone modifications to decipher gene regulatory mechanisms.
  • Metagenomics: Investigating microbial diversity and functions in environmental and clinical samples.

Comparative Analysis of the NovaSeq 6000 and Other Sequencing Systems

Feature NovaSeq 6000 HiSeq 2500 MiSeq NextSeq 500
Throughput Ultra-high (up to 3 Tb) High (up to 1 Tb) Low (up to 15 Gb) Medium-high (up to 120 Gb)
Read Length 50bp to 300bp 50bp to 250bp 50bp to 600bp 75bp to 150bp
Run Time Short (<48 hours) Long (36 hours to 11 days) Short (4 to 55 hours) Medium (~29 hours)
Applications Genomics, transcriptomics, cancer research, single-cell sequencing Genomics, transcriptomics, cancer research Small genomes, 16S rRNA sequencing, targeted sequencing Genomics, transcriptomics, targeted sequencing
Sample Throughput High (multiple samples per run) Medium (multiple samples per run) Low (suitable for a few samples) Medium-high (multiple samples per run)
Instrument Cost High High Low Medium-high
Running Cost High High Low Medium
Data Quality High (high accuracy and consistency) High (high accuracy and consistency) High (high accuracy) High (high accuracy and consistency)

Throughput: The amount of data generated per sequencing run.
Read Length: The number of base pairs read per sequencing read.
Run Time: The time required to complete a sequencing run.
Applications: The fields and uses the system is suitable for.
Sample Throughput: The number of samples that can be processed per run.
Instrument Cost: The cost of purchasing and maintaining the sequencing instrument.
Running Cost: The cost per sequencing run, including reagents and consumables.

For Research Use Only. Not for use in diagnostic procedures.
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