Illumina Novaseq X

Published on April 8, 2024

Novaseq X is a sequencer released by Illumina in January 2023. It is based on Sequencing by Synthesis (SBS).

Illumina Novaseq X
Image of NovaSeq X: https://emea.illumina.com/systems/sequencing-platforms/novaseq-x-plus/order.html by Illumina

Novaseq X is available in the following models:

NovaSeq X - 10B
NovaSeq X - 1.5B
NovaSeq X - 25B

Specifications

Manufacturer	Illumina
Technology	Sequencing by Synthesis (SBS)
Release date	January 2023
Price [2]	$985,000 MSRP as of February 2024
Type	Industrial
Weight	532 Kg
Supports real-time analysis	No
Demultiplexing support	Yes
File format	FASTQ
Read length	Illumina NovaSeq X - 10B: 2x50bp to 2x150bp Illumina NovaSeq X - 1.5B: 2x50bp to 2x150bp Illumina NovaSeq X - 25B: 2x50bp to 2x150bp
Run time	Illumina NovaSeq X - 10B: 18 to 25 hours Illumina NovaSeq X - 1.5B: 17 to 23 hours Illumina NovaSeq X - 25B: 48 hours
Reagent cost per Gb [1]	Illumina NovaSeq X - 10B: $3.20 Illumina NovaSeq X - 1.5B: $5.20 Illumina NovaSeq X - 25B: $2.00
Data quality [3]	Illumina NovaSeq X - 10B: ≥ 90% of bases higher than Q30 Illumina NovaSeq X - 1.5B: ≥ 90% of bases higher than Q30 Illumina NovaSeq X - 25B: ≥ 85% of bases higher than Q30
Maximum output per run (Gb)[4]	Illumina NovaSeq X - 10B: 3000.00 Illumina NovaSeq X - 1.5B: 500.00 Illumina NovaSeq X - 25B: 8000.00
Primary error type [5]	Substitutions

Notes about the specifications

Cost per Gb: The cost per Gb is calculated by dividing the costs of sequencing reagents by the manufacturer’s maximum output per run. For these runs, the manufacturer may have included their own controls and used specific library preparation kits. Actual performance may vary based on sample and library type and quality, loading concentration, and other experimental factors. The sequencing reagent costs used for calculations do not include any other costs associated with preparing the samples or running the instrument, including reagents used for extraction, quality control or library preparation, labor, electricity, lab consumables, storage, etc. Performance metrics and prices are subject to change.
Price: The final price may be different depending on the supplier, the region and any discounts provided through bulk orders or negotiation. Other factors that may influence the final price are warranty options, maintenance contracts, possible trade-ins of older instruments, and any financing arrangements chosen.
Data quality: This is the maximum data quality that the instrument can offer based on manufacturer’s specifications and optimizations. The quality of a specific run will depend on multiple factors, including sample quality, sample quantity, library prep protocol, run conditions, etc.
Maximum output: This is the maximum output of a full instrument run. This number is based on manufacturer’s specifications and optimizations.
Primary error type: This is the most common type of error that may occur due to sequencing. Other types of error may occur as well.

More about the NovaSeq X

The NovaSeq X, launched in 2023 by Illumina, is a next-generation sequencing (NGS) platform targeting the high-throughput sequencing market segment. It succeeds the widely adopted NovaSeq 6000, offering significant improvements in speed and data output while maintaining high accuracy. Notably, the NovaSeq X Plus, a dual-flow cell upgrade, boasts even greater performance.

Key Innovations

The NovaSeq X series introduces several key innovations that translate to faster sequencing runs and increased data output:

XLEAP-SBS Chemistry: This novel sequencing-by-synthesis chemistry represents a significant advancement in sequencing speed. It incorporates nucleotides with improved blocking groups and a more efficient polymerase enzyme. These modifications allow for faster and more accurate nucleotide incorporation and cleavage cycles during the sequencing process. Consequently, XLEAP-SBS chemistry delivers nearly double the sequencing speed and up to three times the accuracy compared to previous chemistries employed in Illumina sequencers, such as those used in the NovaSeq 6000. This translates to a substantial reduction in run times, enabling researchers to complete sequencing projects more quickly.
High-Density Flow Cells: The NovaSeq X utilizes flow cells with a capacity of 10 billion clusters, representing a significant increase compared to the cluster density accommodated by the NovaSeq 6000 flow cells. This increased density allows the NovaSeq X to generate significantly more data per run. For example, the NovaSeq X can produce up to 8 terabases (Tb) of data in a single run, while the NovaSeq 6000 is limited to approximately 3 Tb. This translates to the ability to sequence a higher number of whole genomes, transcriptomes, or exomes per run, making the NovaSeq X ideal for large-scale sequencing projects.
Streamlined Workflow: The instrument incorporates automated processes for library loading, cluster generation, and post-run washing, minimizing hands-on time and potential errors.

Features and Technologies

Improved Data Quality: The XLEAP-SBS chemistry maintains high base calling accuracy (>Q30) despite the increased speed.
Scalability: The NovaSeq X can accommodate various library types and sequencing protocols, offering flexibility for diverse research needs.
User-Friendly Interface: The instrument features a large touchscreen display and intuitive software for simplified run setup and monitoring.

Intended Uses and Specific Applications

The NovaSeq X is well-suited for a broad range of NGS applications due to its high throughput and data quality:

Whole Genome Sequencing (WGS): NovaSeq X is ideal for large-scale WGS projects, including population genomics and clinical diagnostics. Compatible library prep kits include Illumina TruSeq Nano DNA Library Prep Kit and Nextera DNA Flex Library Prep Kit.
Transcriptome Sequencing (RNA-Seq): The platform facilitates deep RNA-Seq analysis for gene expression profiling, alternative splicing detection, and de novo transcriptome assembly. Suitable kits include Illumina TruSeq Stranded mRNA Library Prep Kit and SMARTer Stranded RNA-Seq Kit.
Epigenomics: The NovaSeq X enables high-resolution epigenomic studies like whole-genome bisulfite sequencing for DNA methylation analysis. Library prep options include the MethylationEPIC Kit and the Infinium Assay methylation kits.
Metagenomics: The platform can handle complex metagenomic samples for microbiome analysis and environmental DNA sequencing. Applicable kits include Nextera DNA Flex Library Prep Kit and NEBNext Microbiome DNA Enrichment Kit for sample prep.

Comparison with Competing Instruments

Illumina NovaSeq 6000: The NovaSeq X offers more than double the data output (8 Tb vs. 3 Tb) and faster run times compared to its predecessor, the NovaSeq 6000, at a similar cost.
Complete Genomics DNBSEQ-T7: This competitor boasts faster run times than the NovaSeq X, but with a lower data output per run. Additionally, DNBSEQ-T7 utilizes proprietary chemistries and workflows, potentially limiting flexibility and reagent availability from outside companies.
Complete Genomics DNBSEQ-T20x2: This instrument offers higher data output than the NovaSeq X but with a significantly higher upfront cost, complex workflow and much longer run times.

Special Considerations

Consider the NovaSeq X if you need:

Large-Scale Output: The NovaSeq X excels in projects requiring the sequencing of numerous samples or large genomes, enabling you to generate massive amounts of data in a single run. This translates to faster completion of population-scale genomic studies, deep RNA sequencing, or high-resolution epigenomic analyses.
Rapid Turnaround Time for High Throughput: The increased sequencing speed due to XLEAP-SBS chemistry makes the NovaSeq X ideal for studies where faster results are critical. This can be particularly important for time-sensitive research areas like clinical diagnostics.
Cost-Effectiveness for High Throughput: While a significant investment, the NovaSeq X delivers cost-effective sequencing solutions for consistently high-throughput needs, offering a lower cost-per-gigabyte compared to smaller instruments.
Established Platform: As part of the Illumina sequencing ecosystem, the NovaSeq X leverages the wealth of compatible library prep kits, proven analysis pipelines, and extensive support resources that come with the widely-used Illumina technology.
Flexibility: The adaptability of the NovaSeq X to diverse sequencing applications, such as whole-genome sequencing, transcriptomics, epigenomics, and metagenomics, makes it a versatile solution for multi-faceted research labs.

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This information on this page is up-to-date as of April 8, 2024 and based on the spec sheets published by the manufacturer.