[pmiguel]

We''ll have to wait and see. I have yet to see a bubble on the MiSeq, (although we don't look for one, we have yet to see any spike in the per base N plot of fastqc that we see with HiSeq BMS). So they may have learnt a couple of tricks (like embedding the gaskets on the flow cell).

Alright, different instrument. Probably won't have the issues associated with the HiSeq (bubbles.)

Let's go back to cluster recognition. Looks like 5 initial G's and the cluster will not be seen at all. But, as you mention, that would be less than 0.1% of the amplicons. So the bias would be unlikely to cause issues.

How about 4G's? Do you really think the software would be confident enough of a cluster which only was visible in a single cycle out of the first 5?

How about 3G's?

This whole inferring signal from a lack of signal makes me twitchy...

--
Phillip

[TonyBrooks]

I would bet no such checking is done and bubble covering a cluster get called as "G's".

Alternatively, it is technically possible to eliminate or drastically decrease the number of bubbles that traffic through the flowcell. Illumina has never seemed the least bit interested in doing this, that I could tell. But maybe they have sufficient impetus here to deal with this issue.

--
Phillip

We''ll have to wait and see. I have yet to see a bubble on the MiSeq, (although we don't look for one, we have yet to see any spike in the per base N plot of fastqc that we see with HiSeq BMS). So they may have learnt a couple of tricks (like embedding the gaskets on the flow cell).

[ymc]

Here are some prices I've heard:
FC-404-1002 | NextSeq™ 500 High Output Kit (150 cycles)
List Price (USD):$2,500.00

FC-404-1004 | NextSeq™ 500 High Output Kit (300 cycles)
List Price (USD):$4,000.00

FC-404-1005 | NextSeq™ 500 High Output Kit (75 cycles)
List Price (USD):$1,300.00

For NextSeq High Output PE150, assuming two years shelf life, there can be 365*2*24/29 = 604 run per machine. The per run equipment cost is $250,000/604= $414. Each run costs $4,000. then for a total of 120Gbp output, the cost is $36.78/Gbp.

From a # of read pairs POV, for PE75, 365*2*24/18 = 973 runs per machine. $250,000/973 = $257 equipment cost. $2,500 to run two flow cells. Then for a total of 400M read pairs = $6.89/M read pairs

For HiSeq Rapid PE150, $750,000/(2*365*2*24/39) = $834.76 equipment cost. $7,800 to run two flow cells. Then for an output of 180Gbp, the cost is $47.97/Gbp.

For HiSeq Rapid PE100, $750,000/2*365*2*24/27) = $577.9 equipment cost. $5,800 to run two flow cells. For an output of 600M read pairs = $10.63/M read pairs.

For MiSeq V3 PE300, $100,000/(365*2*24/65) = $371 equipment cost. $1,400 per run. For an output of 15Gbp, the cost is $118/Gbp

For MiSeq V3 PE75, $100,000/(365*2*24/24) = $137 equipment cost. $800 per run. For an output of 25M read pairs, $37.48/M read pairs.

So the conclusion is NextSeq 500 makes sense as expected....

[ymc]

Really nice piece on the computation costs of the HiSeq X Ten:

http://glennklockwood.blogspot.co.uk...=1389835567115

But BGI's 128 HiSeq 2000s have roughly the same output as 10 HiSeq X.

So if they could handle it several years ago, I think the new HiSeq X owners should be ok. It is not like they ordered 100 each this time around.

[Genohub]

Really nice piece on the computation costs of the HiSeq X Ten:

http://glennklockwood.blogspot.co.uk/2014/01/the-1000-genome-computational.html?showComment=1389835567115

[SNPsaurus]

Here are some prices I've heard:
FC-404-1002 | NextSeq™ 500 High Output Kit (150 cycles)
List Price (USD):$2,500.00

FC-404-1004 | NextSeq™ 500 High Output Kit (300 cycles)
List Price (USD):$4,000.00

FC-404-1005 | NextSeq™ 500 High Output Kit (75 cycles)
List Price (USD):$1,300.00

[ymc]

What is the reagent cost for NextSeq 500 High output mode for 2x150 and 2x75? Anyone knows? Thanks

[snetmcom]

There's only so many institutions that can afford/support a Hiseq X. I imagine they were sold so quickly because they were designed specifically for those customers. They probably helped set the spec's of the system.

[ymc]

I think the three buyers of HiSeq X Ten so far probably has a lot of cancer genomes they want to sequence. Now they can go 300x easily. They may also want to run 1000x or more to study tumor heterogeneity.

[ymc]

On our blog we've given our take on Illumina's "$1000" genome and why it still isn't available for most people.

I think it makes sense commercially for them to market it like that in the beginning. Over time, I think lesser players should be able to buy one instead of ten. Application to other species and non-WGS uses should also be available given time.

[pmiguel]

Surely anything beginning with 5 G's won't be registered as a cluster. So bubbles wouldn't contain any clusters either - so you don't get any data. I would expect that there is some algorithm there to detect when something is a G and when it's an intermittent bubble. G's would be localised areas with no signal, bubbles would cover much larger areas.

I would bet no such checking is done and bubble covering a cluster get called as "G's".

Alternatively, it is technically possible to eliminate or drastically decrease the number of bubbles that traffic through the flowcell. Illumina has never seemed the least bit interested in doing this, that I could tell. But maybe they have sufficient impetus here to deal with this issue.

--
Phillip

[AllSeq]

Our take on the "$1000" genome

On our blog we've given our take on Illumina's "$1000" genome and why it still isn't available for most people.

[AllSeq]

Not sure where you got that from or why they would not include the new flow system, chemistry and optics in a machine that was designed to reduce cost and increase throughput. This is from http://www.illumina.com/systems/hise...ng-system.ilmn :

Building on the proven performance of Illumina SBS technology, HiSeq X Ten utilizes a number of advanced design features to generate massive throughput. Patterned flow cells, which contain billions of nanowells at fixed locations, combined with a new clustering chemistry deliver a significant increase in data density (6 billion clusters per run). Using state-of-the art optics and faster chemistry, HiSeq X Ten can process sequencing flow cells more quickly than ever before – generating a 10x increase in daily throughput when compared to current HiSeq® 2500 performance.

I think we're saying the same thing. I agree that the HiSeq X will use the new patterned flow cells. My supposition is that these patterned flow cells will ONLY be for the HiSeq X and it is based on two things:

1) They've only mentioned them for use on the HiSeq X
2) In conversations with people from Illumina (prior to Tuesday's announcement), they said that the patterned flow cells would be restricted to the human whole genomes.

I don't think there is any technical reason to limit these new flow cells to the HiSeq X. I think it's just a marketing decision.

[Chipper]

Ok, thought the post was about the X ten. Why would they not use the two color system for it?

[GenoMax]

Illumina appears to be referring to ordered flowcells as "patterned" flowcells. We need to get used to that term.