NovaSeq from Illumina

[GenoMax]

Illumina just announced a new type of sequencer: NovaSeq

Specifications are here.

NovaSeq 6000 - 6 Tb data/20 billion reads in 2 days
NovaSeq 5000 - 2 Tb data/1.6 billion reads in 2.5 days

Flowcells

S1,S2 - Flowcells for counting applications

For S2 - PF 1775-2070 cluster/mm^2

S3,S4 - High coverage applications

Same cartridges on both sides (three total).

Reagent Cartridge - Will take one library tube (200-300 pM) per FC
SBS Reagents - Frozen
SBS Buffers - Room temperature ship/store. Ready to use.

- FC looks huge, like NextSeq. Easy to place. No futzing needed.

- Run setup identical to current HiSeq sequencers.

- Mix/match flowcells.

- Two sides of the instrument can work independently (stream data to BaseSpace on on side, store locally on other side).

- Automatic post-run wash once sequencing is complete

- Run times includes cluster generation.

- Network speed (200 mbps)

- ONE library pool per flowcell. Lanes visually distinct but fluidically identical

- Both 5000/6000 are dual FC systems. For 5000 systems run times slightly longer

- Custom primers possible

- Asymmetric runs possible (e.g. 100 x 75)

- No "Rapid" run capability needed (Illumina's take)

- FC's can be used for single and paired-end recipes

- ExAMP, all self contained in the sequencer

- 200/240V, adequate HVAC

Test NovaSeq data is available on BaseSpace.

[ngseq]

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

[Genohub]

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/

[luc]

Illumina will of course say it is impossible to do the same with the current sequencers (reduce distances between nanowells).

Similar there seem to be no single end flow cells and only PE150 read kits for two the highest read number flowcells.

[HESmith]

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

Small cores like ours appreciate the flexibility of the 2500, which can accommodate 16 samples per run (minimizing staff time) or two (good for uncommon sequencing requests). It's essentially a 4000 plus NextSeq in one instrument (without the limitations of two-color chemistry associated with the latter), albeit with less data output. Since many of our users already obtain more data per lane than needed (think RNA-Seq/ChIP-Seq with limited number of samples), it's an acceptable tradeoff.

[kmcarr]

Originally Posted by ngseq

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

Our core just bought a new 4000, and by just, I mean installed last week. Explains why Illumina was pushing us all throughout December to get the PO submitted.

[GenoMax]

@kmcarr: Don't mean to sound mean but if you only had the budget for a 4000 then a NovaSeq would likely not have fit in it. After all sequence is sequence, no matter what sequencer model it comes from.

Having seen a string of new sequencers over the years I feel that I would rather have someone else do the bug hunting/fixing in the first year with a new instrument. It may be better to buy the sequencer in the second year, when you are much less likely to face these "growing pains".

If one is going for the "bragging rights" then there is no space for above logic.

[kmcarr]

Originally Posted by GenoMax

@kmcarr: Don't mean to sound mean but if you only had the budget for a 4000 then a NovaSeq would likely not have fit in it. After all sequence is sequence, no matter what sequencer model it comes from.

Having seen a string of new sequencers over the years I feel that I would rather have someone else do the bug hunting/fixing in the first year with a new instrument. It may be better to buy the sequencer in the second year, when you are much less likely to face these "growing pains".

If one is going for the "bragging rights" then there is no space for above logic.

@GenoMax: Yeah I agree, I was just feeling particularly crabby this AM. I'm also remembering the time we sprung for a second GAIIx only to have Illumina Announce the HiSeq a week or two after that order was booked.

And while sequence is sequence regardless of instrument, $/Gbp do matter to researchers. We were loosing business because we had a 2500 as our top instrument and researchers were going elsewhere to get cheaper sequencing done on a 4000. I fear the in a year's time, when enough NovaSeq's are in the field we will be right back in the same boat.

All that said, after digging into the specs (as sparse as they are) it looks to me as though the NovaSeq flow cells are single sample, like the NextSeq. Not a single bit of the literature uses the word "lane". If that is the case then its target market isn't a core like ours. If indeed each flow cell is loaded with a single sample then it would be a nightmare for a core like ours to coordinate multiple projects to fill up one massive sample load.

[GenoMax]

Originally Posted by kmcarr

@GenoMax: Yeah I agree, I was just feeling particularly crabby this AM. I'm also remembering the time we sprung for a second GAIIx only to have Illumina Announce the HiSeq a week or two after that order was booked.

Yikes! You probably know your sales person well by now. It is possible that (s)he may not have been aware of the new sequencer until this week. At least that was my impression from some past conversations.

With AGBT so close, it remains to be seen if we will see another major announcement there.

And while sequence is sequence regardless of instrument, $/Gbp do matter to researchers. We were loosing business because we had a 2500 as our top instrument and researchers were going elsewhere to get cheaper sequencing done on a 4000. I fear the in a year's time, when enough NovaSeq's are in the field we will be right back in the same boat.

That is a true concern. Some institutions subsidize their cores in creative ways and competing fairly (on price) with such cores becomes very hard. Unfortunately these are things that you can't control.

All that said, after digging into the specs (as sparse as they are) it looks to me as though the NovaSeq flow cells are single sample, like the NextSeq. Not a single bit of the literature uses the word "lane". If that is the case then its target market isn't a core like ours. If indeed each flow cell is loaded with a single sample then it would not be a nightmare for a core like ours to coordinate multiple projects to fill up one massive sample load.

Specs talk about 132 exomes/transcriptomes per run so perhaps the idea is to load one single pool (of many) on every run, if there are no independent "lanes" See next post.

Creating a big pool with compatible samples would be a headache for a core as some customers like to make their own libraries to save costs.

[GenoMax]

@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.

[Brian Bushnell]

Originally Posted by ngseq

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.

[Jessica_L]

Originally Posted by GenoMax

@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.

[GenoMax]

Originally Posted by Jessica_L

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]

Originally Posted by GenoMax

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.

[luc]

The specsheet lists 4 wavelengths.

[Jessica_L]

Originally Posted by GenoMax

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]

Originally Posted by Jessica_L

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.