[Jessica_L]

Considering the spec sheet lists 4 lasers this may be incorrect.

It's hard to say. The HiSeq 3000/4000 sheet list the following:

532 nm, 660 nm, 650 nm (barcode reader)

MiSeq uses the 530 nm, 660 nm, too.

The NextSeq sheet has

520 nm, 650 nm; Laser diode: 780 nm, Class IIIb

so I'm not sure what the 780 and 790nm wavelengths on the NovaSeq might be used for...

[Number6]

the announcement from the JP Morgan Healthcare conferene on GenomeWeb describes the NovaSeq as using the two color chemistry

[luc]

" .... the announcement from the JP Morgan Healthcare conferene on GenomeWeb describes the NovaSeq as using the two color chemistry"

Could you point us exactly to where this is stated by illumina?

[GW_OK]

Eco tweeted it. And I think he was there at the presentation?

Anyway, I can't find confirmation either way on the official Illumina pages.

[kmcarr]

For the question regarding flow cell lanes, here's a screencap from the Illumina website. The flow cells definitely have lanes, albeit fewer than the 8 channels for a HiSeq. I assume this is a pic of the S2 flow cells that are actually available, but I also can't tell if the lanes are horseshoe-shaped like a MiSeq.

Having 4 channels doesn't mean they are separate lanes in the same sense as the HiSeq. The NextSeq 500/550 flow cells look just like that with 4 channels yet there is but a single input port so the same sample gets distributed to all 4. These flow cells also look very much like NextSeq flow cells; huge size, surrounded by a plastic frame. The similarity to NextSeq/MiniSeq lends credence to the notion that the NovaSeq supports only 2 color chemistry.

UPDATE: I just got an official, in person confirmation from two Illumina FAS's, the NovaSeq is TWO color chemistry.

[AllSeq]

UPDATE: I just got an official, in person confirmation from two Illumina FAS's, the NovaSeq is TWO color chemistry.

@illumina also just confirmed 2-color via Twitter.

[SNPsaurus]

Mick Watson tweeted:
@BioMickWatson
NovaSeq flowcells have up to 4 lanes but only one loading port :-)

I haven't seen this confirmed, but it is going to be a little tough for facilities that aren't sequencing dozens of large genomes at a time to load single projects that require 3 billion reads. Will a lab wanting to sequence 10 exomes have any use for the Novaseq? Either they team up with other labs and deal with one of them doing something dumb that makes the whole run fail, or they use a S1 chip (will that be as cheap per nuc as S2/3/4?) or continue to use HS2500/4000s.

[GenoMax]

Dr. Keith Robinson talks about NovaSeq in this entry.

As long as Illumina does not discontinue HiSeq 2500, small cores can breath a sigh of relief.

[Jessica_L]

Having 4 channels doesn't mean they are separate lanes in the same sense as the HiSeq. The NextSeq 500/550 flow cells look just like that with 4 channels yet there is but a single input port so the same sample gets distributed to all 4. These flow cells also look very much like NextSeq flow cells; huge size, surrounded by a plastic frame. The similarity to NextSeq/MiniSeq lends credence to the notion that the NovaSeq supports only 2 color chemistry.

UPDATE: I just got an official, in person confirmation from two Illumina FAS's, the NovaSeq is TWO color chemistry.

Thanks for the info and updates, kmcarr. I haven't had a chance to see a NextSeq in action so I didn't realize all the channels loaded from a single input.

[pmiguel]

Biggest change is NovaSeq's reduction in space between nanowells, designed to increase cluster density and data output (up to 2-3x more per flow cell than HiSeq X). Notable is the omission of Nextera based exome and Nextera DNA library prep in the initial compatibility line up.

Summarized specs here: https://blog.genohub.com/2017/01/10/...5000-and-6000/

The only information on reagent costs I've seen were referenced on the Omics Omics blog post:

The BioIT World piece quotes deSouza saying that NovaSeq would be 20% less expensive per gigabase than HiSeq X, 45% cost savings vs. HiSeq 4000 and 50% vs. HiSeq 2500.

Which seems non-nonsensical to me. HiSeq X and HiSeq 3000/4000 flowcells/chemistry seemed very similar, if not identical, and reagent costs for the HiSeq X chemistry was only a little lower (maybe 20%) than HiSeq 3000/4000 costs.

I didn't do a full cost analysis on the HiSeq 3000/4000 reagent cost per gigabase, but it looked like it was about 1/2 that of a HiSeq 2000.

--
Phillip

[pmiguel]

Okay, here is the actual quote from BioIT:

deSouza ran quickly through the comparisons. For a HiSeq 2500 customer, NovaSeq delivers 50% price reduction per Gb; 100% more output per run on the S2 flow cell. For HiSeq 4000 customers, NovaSeq delivers 45% price reduction and 2.5x the output based on the S3 flow cell. For X customers, “NovaSeq will be 20% more economical while delivering three times the throughput.”

So the cost comparison to the HiSeq 2500 is to a NovaSeq S2 flowcell. Whereas the HiSeq 4000 comparison is to a NovaSeq S3 flowcell.

So, if your core can generate enough libraries (dual indexed, I would presume) to make an S3 flowcell run worthwhile, you would generate sequence at 1/4th to 1/3rd the reagent costs of a HiSeq 2500. Even considering the logistical complexities that would entail, it seems like it would be difficult to brush off that kind of a price difference.

I just wish the S1 price per gigabase was going to come in close to that of the S2. But I'm doubting it will.

--
Phillip

[massspecgeek]

I spoke to our Illumina sales rep on the phone yesterday. I was told $30/Gb for S2 100 cycle kits and $15/Gb for 300 cycle. Was also told that 2500 and 3000 are being discontinued effective end of either Q1 or Q2, forgotten which. Our rep hasn't had full briefing yet so I'd be cautious in relying on that, but it's what I've heard so far. Should be getting something in writing this week.

[Brian Bushnell]

I spoke to our Illumina sales rep...Was also told that 2500 and 3000 are being discontinued effective end of either Q1 or Q2, forgotten which. Our rep hasn't had full briefing yet so I'd be cautious in relying on that, but it's what I've heard so far. Should be getting something in writing this week.

Ouch... hope that just means selling new ones, rather than maintaining and supplying existing ones.

[massspecgeek]

Ouch... hope that just means selling new ones, rather than maintaining and supplying existing ones.

Sorry, should have said that support will continue. Only sales of new instruments affected.

[GenoMax]

Sequencing reagents for GAIIx still appear to be available so those who want to keep using their 2500's should be fine.