NovaSeq X and X Plus from Illumina: Latest Sequencing Technologies—Part 1

In the Fall of 2022 Illumina announced their newest pair of flagship sequencers: the NovaSeq X and the NovaSeq X Plus. Their development was part of Illumina’s pursuit of lowering the cost of sequencing by dropping the price to approximately $200 per genome. The major differences between Illumina’s previous top sequencer (the NovaSeq 6000) and the NovaSeq X and X Plus are that the new devices have more affordable and updated reagents, faster run times, and the ability to process data directly on the instrument. Here we’ll take a look at these features and explain how they differ from previous models.

Image of the NovaSeq X (courtesy of Illumina)

Read type and length
Like all Illumina instruments, the NovaSeq X and NovaSeq X Plus are both short read sequencers. The read lengths vary from 2 x 50 bp up to 2 x 150 bp depending on user selection and the choice of the reagent cartridges (options include 100-, 200-, and 300-cycle kits).

Flow cell/SMRT cell options
The three flow cells available with the sequencers (1.5B, 10B, and 25B) are named according to the billions (B) of clusters each are capable of producing. Each flow cell contains 8 independent lanes, which can be used to load 8 separate library pools. The flow cells are patterned like the other production-scale sequencers; however, the improved design positions the nanowells closer together to increase cluster densities and final output. The NovaSeq X only has a single position for a flow cell, but dual flow cell runs are available on the NovaSeq X Plus.


Data output
The output on the NovaSeq X varies from 165 Gb on a run of 2 x 50 bp with a 1.5B flow cell up to 8 Tb on a 2 x 150 bp run using a 25B flow cell. Since the NovaSeq X Plus has two flow cells, the data output varies from 165 Gb up to 16 Tb with a dual flow cell run. This is a significant increase when compared to the 6 Tb of maximum output from the NovaSeq 6000. The number of reads has also increased per flow cell to 26 billion reads on single-end runs and 52 billion on pair-end runs.


Analysis options
The DRAGEN Bio-IT platform is directly built into the sequencers for faster and simpler data analysis. Users now have the ability to analyze their results on the NovaSeq or the option to process the data in the cloud. In addition, genomic data compression is available using DRAGEN ORA (original read archive) in an effort to reduce the time it takes for data transfer and to alleviate storage constraints. The storage footprint can be reduced up to five times while still preserving all the data.

Common applications
● Whole genome sequencing
● Whole exome sequencing
● Whole transcriptome sequencing

Release date
Both instruments won’t be available for shipment until the first quarter of 2023 and some flow cell options won’t be released until later in the year.

Highlights
● An updated chemistry, XLEAP-SBS, with new dyes, linkers, blockers, and a new polymerase to allow for faster incorporation times and an increased stability of reagents.
● Higher data output of up to 16 Tb and a significant reduction in cost per Gb and per read.
● An updated 8-lane flow cell that can support 8 separate library pools compared to the 4 lanes with the NovaSeq 6000.
● Easy and quicker analysis with onboard analysis tools (DRAGEN Bio-IT) and compressed data.
● A more sustainable system with compacted cartridges and lyophilized consumables that don’t need dry ice for shipment.

To compare sequencing technologies please visit Biocompare