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-   -   Lotsa new toys from Illumina: HiSeq X Five, 3000, 4000, NextSeq 550 (http://seqanswers.com/forums/showthread.php?t=49486)

GW_OK 01-12-2015 11:36 AM

Lotsa new toys from Illumina: HiSeq X Five, 3000, 4000, NextSeq 550
 
Hiseq 4000
Hiseq 3000
Nextseq 550
HiseqX 5

http://www.illumina.com/company/news...newsid=2006979

Brian Bushnell 01-12-2015 12:02 PM

Any idea if the HS4000/5000 are using 4-color or 2-color chemistry?

GW_OK 01-12-2015 12:09 PM

I think that's Nextseq only?
Looks to me like they've just stuck HiseqX-style flowcells in the 2500 system.

Brian Bushnell 01-12-2015 12:21 PM

Except that I'm pretty sure the X-series do use 2-dye chemistry, the same as NextSeq...

GenoMax 01-12-2015 12:28 PM

Quote:

Originally Posted by GW_OK (Post 157860)
I think that's Nextseq only?
Looks to me like they've just stuck HiseqX-style flowcells in the 2500 system.

Possible upgrade path for current 2500 owners?

I am not going to hold my breath though.

GW_OK 01-12-2015 12:53 PM

Quote:

Originally Posted by Brian Bushnell (Post 157863)
Except that I'm pretty sure the X-series do use 2-dye chemistry, the same as NextSeq...

Can't find any literature that says anything other than the Nextseq uses 2 colors. In fact, isn't this why the Nextseq currently has GC problems? Haven't heard anything about that with the HiseqX...

GW_OK 01-12-2015 12:54 PM

Quote:

Originally Posted by GenoMax (Post 157864)
Possible upgrade path for current 2500 owners?

I am not going to hold my breath though.


LOL, just like I was able to upgrade my v2-camera 2500's for the v4 chemistry....

westerman 01-12-2015 01:00 PM

New toys for one person is a funding/migration headache for another. Especially if there is no upgrade path. :-(

ECO 01-12-2015 02:29 PM

Made the title more explicit and promoted to the front page...

SNPsaurus 01-12-2015 02:52 PM

This http://blog.illumina.com/blog/illumi...eq-4000-system says the 4000 uses 4-color.

This http://www.illumina.com/content/dam/...0-2014-057.pdf says that 1 flowcell does 50 transcriptomes per run at 50M reads each, so that is >300M reads per lane. Looks faster as well, if the longest run time is 3.5 days (not sure if that would be for 1x150bp or 2x150bp).

nucacidhunter 01-12-2015 03:06 PM

There are data from PCR-free, RNA-Seq and NRC libraries sequenced on HiSeq 4000 in BaseSpace.

SNPsaurus 01-12-2015 03:35 PM

Heard from someone that the cluster and reagent kits are similar in price to current Hiseq 2000 reagents, which would mean the price per read is quite a bit lower.

HeinKey 01-13-2015 05:56 AM

#SNPsaurus:
I assume it will be 2x 150 bp in 3.5 days.
2.1 to 2.5 billion clusters per flow cell, in a 2x150 bp run is 630 - 750 Gb.
With a speed >200Gb per day a 2x 150 bp run will take 3.5 days.

I wonder if we can upgrade the 2500 V4 machine to a 4000 version...

kmcarr 01-13-2015 06:23 AM

It looks to me that the 3000/4000 only accept 8 lane flow cells (high-output). If true then the trade off for throughput is flexibility.

austinso 01-13-2015 08:01 AM

Quote:

Originally Posted by GenoMax (Post 157864)
Possible upgrade path for current 2500 owners?

I am not going to hold my breath though.

Ditto. I think supporting the patterned flow-cells would require too much of a reworking of the guts...

Seems like they are following the Apple product release model...

AllSeq 01-13-2015 09:43 AM

Quote:

Originally Posted by Brian Bushnell (Post 157863)
Except that I'm pretty sure the X-series do use 2-dye chemistry, the same as NextSeq...

The X series uses the standard 4-dye chemistry. NextSeq is the only one to use 2-dye. (And the one that people seem to be having the most problems with in terms of quality...)

GenoMax 01-13-2015 09:54 AM

Quote:

Originally Posted by austinso (Post 157945)
Seems like they are following the Apple product release model...

More like Intel model. e.g. socket LGA2011 --> LGA2011-v3 (not backwards compatible).

FWOS 01-13-2015 09:57 AM

Pretty sure they will initially only support 2x125 in 3.5 days

Genohub 01-13-2015 08:35 PM

"The 3000 is to the 4000 as the 1000 was to the 2000 and the 1500 to the 2500" Nice summary here: https://biomickwatson.wordpress.com/...00-in-context/

- Genohub

SNPsaurus 01-13-2015 10:18 PM

The one difference with these machines is the throughput. A university facility needed 2 flow cells that could be run independently to help manage a queue, since a paired end run would be almost two weeks (less now). But if most runs are 1-3 days, then that is less of a problem. I suspect the 3000 won't be substantially cheaper so it won't be appealing since you might as well get twice the capacity for a little extra, but some of the other reasons are less important for these machines.

jwfoley 01-14-2015 08:21 AM

I know nobody here cares about microarrays (nor should we?), but I think Illumina deserves some serious mad-scientist points for the NextSeq 550. If I'm understanding correctly, they've made a microarray adapter that fits in the flow-cell slot, and are reading it with the same scanner. More innovation than I'd expect from a company with a secure monopoly.
http://www.illumina.com/content/dam/...-550-array.jpg
Maybe this is an attempt to wean the last few stragglers off arrays and get them into sequencing?

HeinKey 01-15-2015 05:20 AM

Can these new flow cells still be overloaded, or has Illumina created the ideal clustering procedure? Just load your library at high concentration for maximal occupance of the flow cell "wells" and skip qPCR and titration.....
Anything known about the clustering procedure yet?

GW_OK 01-15-2015 07:22 AM

1 Attachment(s)
Remembering back to the HiseqX announcement the little holes that now hold the clustering oligos (which is why this is a "patterned" flowcell) allow 1 oligo to overpower any others that try to cluster in there. I suppose you could somehow get it to overcluster but it wouldn't be the same kind of overclustering we are used to.

Clustering still appears to be on the cBot.

Here's some back-of-excel calcs I did on prices posted for the new 3k/4k reagents. Throughput assumptions are made based on average numbers given by Illumina in their specs and 8-lane FCs.

Attachment 3529

nucacidhunter 01-15-2015 07:53 PM

Quote:

Originally Posted by HeinKey (Post 158162)
Can these new flow cells still be overloaded, or has Illumina created the ideal clustering procedure? Just load your library at high concentration for maximal occupance of the flow cell "wells" and skip qPCR and titration.....
Anything known about the clustering procedure yet?

They still need to be quantified. Assuming similarity of HiSeq 4000 flow cell to HiSeq x, they can be overloaded which will reduce the reads %PF. Low loading will increase the number of duplicate reads. Illumina manual also states that underloading can reduce or result in unacceptable %PF. Loading is depend on library type (Nano or PCR-free).

ymc 01-16-2015 08:07 PM

No rapid mode is a bummer for HiSeq 4000. I hope they can add that later.

I also want an upgrade of MiSeq

ymc 01-18-2015 04:19 AM

Looks like there will be a V2 chemistry coming soon for NextSeq. Illumina claimed that the error rate can be on par with MiSeq/HiSeq. Hope this is true. This can be a nice upgrade for MiSeq.

HiSeq 4000 is quoted at $900K and 2500 is reduced to $690K. Both are more expensive than I expect.

matth431 01-20-2015 02:01 AM

Quote:

Originally Posted by HeinKey (Post 157932)
#SNPsaurus:
I assume it will be 2x 150 bp in 3.5 days.
2.1 to 2.5 billion clusters per flow cell, in a 2x150 bp run is 630 - 750 Gb.
With a speed >200Gb per day a 2x 150 bp run will take 3.5 days.

I wonder if we can upgrade the 2500 V4 machine to a 4000 version...

I asked Illumina and was told not. Apparently the cameras are more sensitive.

Also, the NextSeq550 capability for arrays is currently limited to the methylation and karyomapping chips, not sure why. They have suggested they may look into allowing iSelect if enough users are interested. Personally, I feel it would be a good move - core labs could use the NextSeq as a stopgap for priority NGS/genotyping runs if the HiSeqs/iScans are at capacity or down for repair.

ymc 01-21-2015 11:36 PM

http://www.illumina.com/systems/next...ncer/kits.html

I see NextSeq V2 kits here claiming better error rate than v1. Is it true?

The throughput is the same??

HeinKey 01-22-2015 06:48 AM

just visited an Illumina meeting in Brussels.

Current HiSeqs are not upgradable to the 3000 or 4000 versions. Hardware is too different between the systems.

4000 and 3000 can only sequence Human DNA with certain fragment length. WGS, exome and RNAseq will work well, other library types are not supported due to the limitations of the new exclusion amplification kinetics.

New NextSeq V2 chemistry was presented. New dyes in the V2 kits with much less spectral overlap compared to the V1 dyes. Discrimination between dyes is much better resulting in higher quality reads and lower error rates. Now comparable with their four dye chemistry.
All in all very informative again.

GenoMax 01-22-2015 07:50 AM

Quote:

Originally Posted by HeinKey (Post 158601)
Current HiSeqs are not upgradable to the 3000 or 4000 versions. Hardware is too different between the systems.

No surprise there.

Quote:

Originally Posted by HeinKey (Post 158601)
4000 and 3000 can only sequence Human DNA with certain fragment length. WGS, exome and RNAseq will work well, other library types are not supported due to the limitations of the new exclusion amplification kinetics.

I highly doubt 4000/3000 are going to be limited to human samples only (DNA with certain fragment size perhaps because of ordered flowcells).

GenoMax 01-22-2015 10:27 AM

From: http://www.illumina.com/systems/hise...lications.html

Quote:

The HiSeq 3000/HiSeq 4000 Systems deliver the highest daily throughput and lowest price per sample for multiple applications, species, and sample types, providing an ideal solution for production-scale sequencing labs.
Looks like no restrictions on sample types for 3000/4000.

cement_head 01-22-2015 12:32 PM

Quote:

Originally Posted by HeinKey (Post 157932)
#SNPsaurus:
I assume it will be 2x 150 bp in 3.5 days.
2.1 to 2.5 billion clusters per flow cell, in a 2x150 bp run is 630 - 750 Gb.
With a speed >200Gb per day a 2x 150 bp run will take 3.5 days.

I wonder if we can upgrade the 2500 V4 machine to a 4000 version...

Dumbass Question Alert, but does 2.1 billion clusters = 2.1 billion reads? Or would that be 2.1 billion clusters and with PE be 4.2 billion reads?

I guess my real question is on the HiSeq3000, how many reads do I get with 2x150bp PE?

Thanks in advance...

GenoMax 01-22-2015 01:00 PM

Quote:

Originally Posted by cement_head (Post 158626)
Dumbass Question Alert, but does 2.1 billion clusters = 2.1 billion reads? Or would that be 2.1 billion clusters and with PE be 4.2 billion reads?

Yes. That is how illumina counts them.

Quote:

Originally Posted by cement_head (Post 158626)
I guess my real question is on the HiSeq3000, how many reads do I get with 2x150bp PE?

Thanks in advance...

Here are published specs (I assume you are interested in total sequence rather than number of reads): http://www.illumina.com/systems/hise...fications.html

andibody 01-23-2015 12:47 AM

Our sales rep claimed there are no single read cluster kits available (yet) for HS3000/4000. Can anyone confirm? Sounds like a strange decision (if true) to me.

GenoMax 01-23-2015 05:35 AM

Quote:

Originally Posted by andibody (Post 158675)
Our sales rep claimed there are no single read cluster kits available (yet) for HS3000/4000. Can anyone confirm? Sounds like a strange decision (if true) to me.

That probably means "for the time being" ... as manufacturing is ramped up for new reagents/flowcells. Specifications list a 1x50 run, so single end kits may be coming in future (http://www.illumina.com/systems/hise...fications.html).

cement_head 01-23-2015 07:14 AM

Quote:

Originally Posted by GenoMax (Post 158631)
Yes. That is how illumina counts them.



Here are published specs (I assume you are interested in total sequence rather than number of reads): http://www.illumina.com/systems/hise...fications.html

No, I'm interested in total number of reads to calculate coverage.

So, what this (thread) is saying, is that for the same amount of money on a HiSeq2500 RR, if I did the run on a HiSeq3000 - I can potentially get >10x the amount of reads?

HiSeq2500 360M reads

HiSeq3000 4.2B reads

Have I got this right? If so, this is amazing!

jwfoley 01-23-2015 07:22 AM

That's not really so amazing. A HiSeq 2500 in High Output mode will give you more than 6X as many reads (2 billion is the spec for v4). Rapid Run isn't for people who care about cost-effectiveness.

SNPsaurus 01-23-2015 10:38 AM

My understanding is the the HiSeq 4000 per lane cost will be similar to the per lane cost of the HiSeq 2500. At our local facility, the per lane cost is similar for high-output or rapid run on the HiSeq 2500. So I would say roughly the same costs for:
HiSeq 2500 high-output 200M reads per lane (8 lanes per run)
HiSeq 2500 rapid run 180M reads per lane (2 lanes per run)
HiSeq 3/4000 320M reads per lane (8 lanes per run)

andibody 01-25-2015 10:43 AM

There should be an exact max of clusters for HiSeq 3000/4000 defined by the number of microwells (325M as stated above?).
We're getting regularly 300M reads on the upgraded 2500. If 325M is correct, the increase is not very pronounced if the shortened run durations are not countered in.

kmcarr 01-25-2015 11:05 AM

Quote:

Originally Posted by andibody (Post 158819)
There should be an exact max of clusters for HiSeq 3000/4000 defined by the number of microwells (325M as stated above?).
We're getting regularly 300M reads on the upgraded 2500. If 325M is correct, the increase is not very pronounced if the shortened run durations are not countered in.

Are you sure you are comparing the same numbers (read, clusters, lanes, flow cell)? And for the HiSeq 2500 numbers are you talking about Rapid Run or V4 High Output?

The HiSeq 3000/4000 specs are 325M clusters per lane, which would be 650M reads per lane for paired end runs (using Illumina's method of counting).

The HiSeq 1500/2500 specs are 250M clusters per lane for V4 High Output (500M reads per lane). Our experience is pushing even slightly past 280M clusters per lane results in dramatic decreases in %PF and read quality.

andibody 01-26-2015 02:01 AM

High Output.
True, it's more like 270-290M with Q>30.
Still, it's 'only' a 15% increase. (again, not countering in speed and evenness of cluster density).

pmiguel 01-26-2015 08:52 AM

Quote:

Originally Posted by cement_head (Post 158725)
No, I'm interested in total number of reads to calculate coverage.

So, what this (thread) is saying, is that for the same amount of money on a HiSeq2500 RR, if I did the run on a HiSeq3000 - I can potentially get >10x the amount of reads?

HiSeq2500 360M reads

HiSeq3000 4.2B reads

Have I got this right? If so, this is amazing!

No, at best you may be looking at 1.5X the amount of sequence per $. (That 4.2B reads figure is likely for an entire flowcell.)

My guess is it will be slightly less than this as Illumina always combines an improvement in instrumentation/chemistry with an increase in reagent costs.

Plus there is the cost of the new instrument itself that may contribute to the cost of the service.

--
Phillip

kcchan 01-26-2015 12:56 PM

The difference is even less if you compare HiSeq 2500 V4 to HiSeq 4000. The HiSeq 4000's specs claim 4.3-5B reads vs up to 4B reads on a HiSeq 2500. After factoring in instrument and overhead costs I would imagine that pricing for the 4000 runs may be higher for the first 6-12 months.

pmiguel 01-27-2015 07:18 AM

Quote:

Originally Posted by kcchan (Post 158869)
The difference is even less if you compare HiSeq 2500 V4 to HiSeq 4000. The HiSeq 4000's specs claim 4.3-5B reads vs up to 4B reads on a HiSeq 2500. After factoring in instrument and overhead costs I would imagine that pricing for the 4000 runs may be higher for the first 6-12 months.

Yes, I think maybe the main benefit from the 3000/4000 over a 2500-1T running v4 chemistry would be less worries about overclustering a flow cell. And that is big--on a psychological level. But I think most cores have systems in place that either make this rare or just leave it up to the customers to send correctly titred libraries.

--
Phillip

Chipper 01-27-2015 10:15 AM

Increased throughput (reduced run time) appears to be the main thing. Would be nice if it translates to reduced costs but for that I think they need some serious competiton (BGI, not PII...).

Hiseq2500: 450-500 Gb, 6 days 4000: > 400 Gb/day

Ingeneious 01-27-2015 11:32 AM

Quote:

Originally Posted by jwfoley (Post 158049)
I know nobody here cares about microarrays (nor should we?), but I think Illumina deserves some serious mad-scientist points for the NextSeq 550. If I'm understanding correctly, they've made a microarray adapter that fits in the flow-cell slot, and are reading it with the same scanner. More innovation than I'd expect from a company with a secure monopoly.
http://www.illumina.com/content/dam/...-550-array.jpg
Maybe this is an attempt to wean the last few stragglers off arrays and get them into sequencing?

They had the HiScanSQ that did arrays plus sequencing and that was quickly discontinued. Asked an Illumina employee about it and he said it seemed like they were trying to make peanut butter and jelly again - he couldn't figure out the logic in it either.

It's cheaper than the NextSeq 500 and iScan combined, so might be useful for research labs looking for a sequencer and array as well or those doing scanning as followups. Seems very niche though.

pmiguel 01-27-2015 12:10 PM

Quote:

Originally Posted by Chipper (Post 158966)
Increased throughput (reduced run time) appears to be the main thing. Would be nice if it translates to reduced costs but for that I think they need some serious competiton (BGI, not PII...).

Hiseq2500: 450-500 Gb, 6 days 4000: > 400 Gb/day

Slight correction:
A HiSeq2500 1T should be able to do 500 GB per flowcell in 6 days. (83Gb/day) A HiSeq4000 can do about 700Gb per flowcell in 3.5 days (200Gb/day).

Still, a major increase!

--
Phillip

Genohub 01-27-2015 07:53 PM

Looks like most of the points on the latest Illumina tech have been covered in this thread. A few others points that I haven't seen covered yet:

- HiSeq 3000 will cost around the same as HiSeq 2500 v4.
- HiSeq 3000 is upgradeable to HiSeq 4000 (the HiSeq v4 upgrade was only available on instruments that shipped after 2013).
- You can upgrade from X Five to X Ten...just buy more instruments, but at the lower $1M/instrument cost.
- Illumina is going to start bundling library prep and cluster reagents on the X series.
- X series is still only for whole human WGS...likely to focus battle w/ the BGI / CG WGS instrument release later this year or a good excuse to release more patterned flow cell models....

We've written some more details about the new release here: http://blog.genohub.com/illuminas-la...-and-hiseq-x5/.

As a platform that regularly handles sequencing service listings and orders, Genohub collects a lot of information on price and changes in price once a new instrument is released. In general, we've noticed what others have posted in this thread, price per Gb is rarely more competitive immediately after an instrument is released. There are still many providers offering excellent turnaround times and prices on HiSeq services that will continue to be competitive even after we have our first HiSeq 3000/4000 listed on Genohub.

pmiguel 01-28-2015 06:35 AM

Quote:

Originally Posted by Genohub (Post 158992)
- HiSeq 3000 is upgradeable to HiSeq 4000 (the HiSeq v4 upgrade was only available on instruments that shipped after 2013).

HiSeq 3000 is to HiSeq 4000 as HiSeq 1500 was to HiSeq 2500. 1 flow cell vs 2 flow cells.

The "1T" upgrade available to newer HiSeqs, that allows use of v4 chemistry, was independent of whether they had 1 or 2 flow cells.

--
Phillip

austinso 01-28-2015 10:05 AM

FWIW...I think the Q4 results transcripts say a lot more about Illumina's product roadmap:

http://www.seekingalpha.com/article/2856246

1. HiSeq2500 is being removed from FDA clearance, and will be replaced with the NextSeq with NIPT.

2. HiSeq3000 effectively replaces the HiSeq2500...not the HiSeq4000.

3. rapid mode will not be supported by either the HiSeq3000/4000.

Bright shiny objects usually have a purpose...

pmiguel 01-28-2015 12:21 PM

Quote:

Originally Posted by austinso (Post 159044)
2. HiSeq3000 effectively replaces the HiSeq2500...not the HiSeq4000.

In the sense that a 3000 will produce about the same amount of sequence per unit time as a 2500-1T. Also in the sense that Illumina priced the 3000 at the current 2500 price.
But in the sense that the 2500 is a 2 flow cell instrument it would be replaced by the 4000 as a 3000 has only one flow cell.
Quote:

3. rapid mode will not be supported by either the HiSeq3000/4000.
I only see this from Jay Flatley to support your statement:
Quote:

There will be a number of customers who remain on the 2500, however, due to the use of validated workflows or the importance of access to rapid run mode and longer reads.
But this doesn't imply that rapid chemistry will never be available on the 3000/4000, does it?

--
Phillip

austinso 01-29-2015 02:37 PM

Quote:

Originally Posted by pmiguel (Post 159054)
In the sense that a 3000 will produce about the same amount of sequence per unit time as a 2500-1T. Also in the sense that Illumina priced the 3000 at the current 2500 price.

But in the sense that the 2500 is a 2 flow cell instrument it would be replaced by the 4000 as a 3000 has only one flow cell.

And in the sense that the people who bought the 2500 in Q4 will be potentially be offered a 3000 and not a 4000. I'm entertaining the Illumina POV here...

Quote:

But this doesn't imply that rapid chemistry will never be available on the 3000/4000, does it?
Correct, it doesn't, so yes I'm reading between the lines here...

I'd say given the push for the NextSeqDx, and dropping the HiSeq2500 for 510(k) clearance, it makes less sense to introduce rapid mode capacity (or even maintain for the 2500) for the 3000/4000 when there is a NextSeq500 that is being pushed as a product.

Besides, I don't think that ordered clustering is something that can be pushed in the same kind of way any time soon...

IMHO, of course...

frozenlyse 02-03-2015 07:07 PM

Quote:

Originally Posted by pmiguel (Post 158972)
Slight correction:
A HiSeq2500 1T should be able to do 500 GB per flowcell in 6 days. (83Gb/day) A HiSeq4000 can do about 700Gb per flowcell in 3.5 days (200Gb/day).

Still, a major increase!

--
Phillip

Which means that people will be doing more runs per year which means a lot more reagent sales for Illumina!

DNATECH 05-21-2015 12:30 AM

Some HiSeq3000 data are analyzed in this thread:
http://seqanswers.com/forums/showthread.php?t=58353


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