Our sequencing core is planning on upgrading from the Novaseq 6000 to Novaseq X Plus
There is obviously a substantial price drop per lane and an increase the number of sequences you can get per lane.
What I am wondering is:
Has anyone has compared the quality of the sequencing data from the two platforms?
Is there any difference in the downstream analysis? I'm assuming they are interchangeable since they are both from Illumina and would generate similar FASTQ data formats
Does your core has the volume to fill it regularily? What I like about local cores is that despite a bit more expensive than large ones they sre flexible and fast. But that only works with smaller sequencers where you don't have to wait for the lanes to be filled. I see these super large scale sequencers in large facilities that also do their own libraries so they can multiplex as needed and have it filled at all times. For smaller cores you probably better off with Nextseqs.
If past history can be used as a guide, there will likely be little difference in terms of quality especially between NovaSeq 6000 and X. Looks like X uses a new chemistry that is still 2-color so the improvements are likely in speed. Illumina has maintained a stance that the sequence their sequencers generate is equivalent irrespective of model/chemistry etc.
You core may face a bigger internal change to keep the monster fed. Since they are going ahead with the change they have likely made the calculations related to that and determined that going large makes practical sense (beyond the marketing hype).
If your core currently uses bcl2fastq for post-processing of data then they will end up having to switch to bcl-convert (which supports all older sequencers) since that would probably be a requirement for processing data from NovaSeq X. If built in DRAGEN FPGA is used then you would also be able to generate Original Read Archive (ORA) files that supposedly compress 5x better but are likely not natively supported by other software. Illumina does provide a conversion tool from what I recall.
If you have long running projects then doing your own internal validation (re-running a set of selected samples that have previously run on NovaSeq 6000 and checking concordance) would likely be the best way to convince everyone that the change would not cause a batch (or any) effect.
Does your core has the volume to fill it regularily? What I like about local cores is that despite a bit more expensive than large ones they sre flexible and fast. But that only works with smaller sequencers where you don't have to wait for the lanes to be filled. I see these super large scale sequencers in large facilities that also do their own libraries so they can multiplex as needed and have it filled at all times. For smaller cores you probably better off with Nextseqs.