[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

[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.

[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.

[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.

[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.

[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.

[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.

[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?

[Number6]

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

[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...

[luc]

The specsheet lists 4 wavelengths.

[Jessica_L]

From the blog link that Genohub posted in #3:

@Genohub: How confident are you about that?

That was going to be my next question.

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.

[GenoMax]

Where did you see that it's two color? The spec sheet lists four different laser wavelengths (532, 660, 780, 790nm), so I was hopeful they were going back to that.

From the blog link that Genohub posted in #3. Considering the spec sheet lists 4 lasers this may be incorrect.

Two color or Four color chemistry: Two color, like the NextSeq 500

@Genohub: How confident are you about that?

[Jessica_L]

@Genohub blog (from post #3) indicates following:

2 "lanes" for S1,S2 flowcells and 4 for S3,S4. S1,S2 only compatible with NovaSeq 5000 and S1-->S4 for NovaSeq 6000.

NovaSeq is using TWO color chemistry. Could be a concern for some.

Where did you see that it's two color? The spec sheet lists four different laser wavelengths (532, 660, 780, 790nm), so I was hopeful they were going back to that.

[Brian Bushnell]

With Novaseq now on the market, who is still going to buy HiSeq 2500/3000/4000/X?

I would still go with a 2500. For our purposes, analyst time wasted on low-quality data is more expensive than generating higher-quality data in the first place, when the cost of sequence is in the same ballpark.