MiSeq - Page 2

james hadfield · 01-14-2011, 06:42 AM

I was wondering if it might be possible to get even more fomr this box of tricks by daisychaining some of the internals.

Right now the imaging module is the most expensive bit in a GA or HiSeq. This is probably the same for MiSeq. As imaging takes 30sec compared to five mnutes for chemistry why not simply have six fluidics modules and put six 10 tile single lane flowcells on, or just one. All would be imaged by the same module just like HiSeq.

MiSeq 2000. You heard it here first ;-)

James.

genlyai · 01-14-2011, 06:50 AM

So have we heard anything about $/run and how that compares with Ion Torrent? If that's comparable, this seems like it's going to crush Ion, mainly because of Nextera prep.

nickloman · 01-14-2011, 10:01 AM

$400 - $750 per run apparently.

genlyai · 01-14-2011, 10:16 AM

Thanks, Nick. I see now that that was on your first blog post. Is that price inclusive of library prep?

If so, MiSeq is winning on every metric -- not least that it will use the exact same libraries as the big machine. As someone else said, it's not really in our interest for Illumina to leave its competition in the dust, but that's what seems likely here.

Assuming the machine meets these specs. I guess we do know by now that that's a big assumption.

GW_OK · 01-14-2011, 11:03 AM

Quote:

Originally Posted by james hadfield

Anyone want to bet on how high Illumina are going to predict HiSeq will go by the end of 2011?

My pick in the sweepstake is 2Tb, it is HiSeq 2000 after all!

I'd bet a dollar it'll be 1Tbp by summertime, so you might be right...

nickloman · 01-14-2011, 11:45 AM

Quote:

Originally Posted by genlyai

Thanks, Nick. I see now that that was on your first blog post. Is that price inclusive of library prep?

Not sure, perhaps not - but a single library prep with Nextera is pretty cheap I believe (? £30 per sample).

nickloman · 01-14-2011, 11:46 AM

Quote:

Originally Posted by GW_OK

I'd bet a dollar it'll be 1Tbp by summertime, so you might be right...

They did a 1.17Tb run already at Illumina HQ, I believe!!

What an amazing time this is!

GW_OK · 01-14-2011, 03:00 PM

Quote:

Originally Posted by nickloman

They did a 1.17Tb run already at Illumina HQ, I believe!!

What an amazing time this is!

Yes, but it's not supported and in our hands. It should be by summer.

GERALD · 01-19-2011, 09:44 AM

It sounds like the same reagents on a lower capacity machine. I think many labs would rather not go to the trouble, especially when you consider that the amount of labor is the same. Also, any word about machine cost? I get the feeling they are trying to compete with IonTorrent.

genlyai · 01-19-2011, 10:46 AM

Quote:

Originally Posted by GERALD

It sounds like the same reagents on a lower capacity machine. I think many labs would rather not go to the trouble, especially when you consider that the amount of labor is the same. Also, any word about machine cost? I get the feeling they are trying to compete with IonTorrent.

Well, consider the sample prep will supposedly be a matter of a few hrs with a few minutes of hands-on time. Meanwhile the run time, cost per run, and upfront cost are much smaller. There are definitely applications, not least (as Keith Robison always says) validating libraries before they go to the big machine.

krobison · 01-19-2011, 01:34 PM

Quote:

Originally Posted by GERALD

It sounds like the same reagents on a lower capacity machine. I think many labs would rather not go to the trouble, especially when you consider that the amount of labor is the same.

For a lab that already has a HiSeq or IIx, you are probably correct -- the cost per base (even amortizing in the machine) will be significantly higher on the MiSeq.

But, for someone not yet in that game, it is a very interesting machine -- particularly if $125K makes people furrow their brow but $500+K causes them to stop taking you seriously.

ALSO, note the run times. For some applications, being able to go from sample DNA to data in a matter of hours or just over a day (depending on the read length & amount of data you need) is critical. I suspect that even some labs well practiced with the "big iron" will consider a MiSeq if they have applications requiring fast turnaround or to do small method-development projects.

Quote:

Originally Posted by GERALD

Also, any word about machine cost? I get the feeling they are trying to compete with IonTorrent.

$125K, for a complete package. Very similar to what is claimed for Ion Torrent once you throw in necessary accessories. And not just Ion Torrent, but 454 Jr (and to some degree PacBio, given PacBio was going to offer fast runs cheaply -- ignoring the amortization cost of the instrument).

genlyai · 01-19-2011, 01:43 PM

Exactly, we don't have a HiSeq, we won't be buying a HiSeq. We send our stuff out because we don't have that much of it.

But we do make some unusual libraries from time to time. From time to time we try to run a sketchy sample. It is really annoying to wait 4-6 weeks to find out if it worked. (It would even be annoying to wait 5-10 days for the big machine to run if we had it on hand.)

ymc · 01-19-2011, 11:44 PM

Can MiSeq be used for full exome sequencing in one run???

krobison · 01-20-2011, 05:47 AM

Illumina is claiming just under a Gigabase in the 2x150 mode. For a 50Mb human exome capture, that would be only 20X coverage, which seems like a bit of an undershoot.

On the other hand, with a 5Mb custom capture design it would be 200X average coverage, which would seem doable (what are folks shooting for these days?).

ymc · 01-20-2011, 06:14 PM

Quote:

Originally Posted by krobison

Illumina is claiming just under a Gigabase in the 2x150 mode. For a 50Mb human exome capture, that would be only 20X coverage, which seems like a bit of an undershoot.

On the other hand, with a 5Mb custom capture design it would be 200X average coverage, which would seem doable (what are folks shooting for these days?).

Thanks for your reply. How many x of coverage is required to reach the genotyping accuracy of the microarray chips?

Vinz · 01-21-2011, 06:39 AM

Sounds like a great instrument!
Whats your bet on read length? Do you think Illumina is at the limits of the chemistry with the 2x150bp?

avilella · 01-28-2011, 03:22 AM

Has anyone done the math on the price per base one would get with a 2x150bp run on the MiSeq and the HiSeq, taking into account library prep costs?

People working medium-sized genomes (10-100 MBp) sometimes spend a lot of time and effort getting clean clonal DNA, so doing a try on the MiSeq would be great for them, but maybe they can wait to do 1 lane on the HiSeq if there is not much price difference...

genlyai · 01-28-2011, 05:46 AM

The price per base difference will vastly favor HiSeq, but I'm not sure that's the metric you would care about if you want to quickly test the quality of your library & DNA. Wouldn't you just care about turn-around time and cost per run?

vebaev · 02-16-2011, 04:10 AM

Hi,
our lab have used only sequencing services for mRNA-seq and smallRNAs seq with Illumina GA (for plant samples).
We are quite interesting to get MiSeq since we do not have sequencer, is there any limitations that MiSeq have that we have to know before buying it?

Thanks

vebaev · 02-19-2011, 02:09 AM

Since the covarage of MiSeq will be smaller than GA is it possible to use it for sequencing of transcriptomes (mRNA-seq, plant species in my case)? If not whole transcriptome is it possible to catch at least most abundant transcripts?

The same for genome sequencing? is it possible to catch part of the genome with Miseq (again plant genome) and If needed to make more runs for more covarage of the genome?

Thanks!

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01-14-2011, 06:42 AM	#21
james hadfield Moderator Cambridge, UK Community Forum Location: Cambridge, UK Join Date: Feb 2008 Posts: 221	I was wondering if it might be possible to get even more fomr this box of tricks by daisychaining some of the internals. Right now the imaging module is the most expensive bit in a GA or HiSeq. This is probably the same for MiSeq. As imaging takes 30sec compared to five mnutes for chemistry why not simply have six fluidics modules and put six 10 tile single lane flowcells on, or just one. All would be imaged by the same module just like HiSeq. MiSeq 2000. You heard it here first ;-) James.

01-14-2011, 06:50 AM	#22
genlyai Member Location: Boston, MA Join Date: Aug 2009 Posts: 39	So have we heard anything about $/run and how that compares with Ion Torrent? If that's comparable, this seems like it's going to crush Ion, mainly because of Nextera prep.

01-14-2011, 10:01 AM	#23
nickloman Senior Member Location: Birmingham, UK Join Date: Jul 2009 Posts: 356	$400 - $750 per run apparently.

01-14-2011, 10:16 AM	#24
genlyai Member Location: Boston, MA Join Date: Aug 2009 Posts: 39	Thanks, Nick. I see now that that was on your first blog post. Is that price inclusive of library prep? If so, MiSeq is winning on every metric -- not least that it will use the exact same libraries as the big machine. As someone else said, it's not really in our interest for Illumina to leave its competition in the dust, but that's what seems likely here. Assuming the machine meets these specs. I guess we do know by now that that's a big assumption.

01-19-2011, 09:44 AM	#29
GERALD Member Location: San Francisco, CA Join Date: Jun 2010 Posts: 20	It sounds like the same reagents on a lower capacity machine. I think many labs would rather not go to the trouble, especially when you consider that the amount of labor is the same. Also, any word about machine cost? I get the feeling they are trying to compete with IonTorrent.

01-19-2011, 01:43 PM	#32
genlyai Member Location: Boston, MA Join Date: Aug 2009 Posts: 39	Exactly, we don't have a HiSeq, we won't be buying a HiSeq. We send our stuff out because we don't have that much of it. But we do make some unusual libraries from time to time. From time to time we try to run a sketchy sample. It is really annoying to wait 4-6 weeks to find out if it worked. (It would even be annoying to wait 5-10 days for the big machine to run if we had it on hand.)

01-19-2011, 11:44 PM	#33
ymc Senior Member Location: Hong Kong Join Date: Mar 2010 Posts: 498	Can MiSeq be used for full exome sequencing in one run???

01-20-2011, 05:47 AM	#34
krobison Senior Member Location: Boston area Join Date: Nov 2007 Posts: 747	Illumina is claiming just under a Gigabase in the 2x150 mode. For a 50Mb human exome capture, that would be only 20X coverage, which seems like a bit of an undershoot. On the other hand, with a 5Mb custom capture design it would be 200X average coverage, which would seem doable (what are folks shooting for these days?).

01-21-2011, 06:39 AM	#36
Vinz Member Location: Germany Join Date: Dec 2010 Posts: 80	Sounds like a great instrument! Whats your bet on read length? Do you think Illumina is at the limits of the chemistry with the 2x150bp?

01-28-2011, 03:22 AM	#37
avilella Member Location: uk Join Date: Mar 2009 Posts: 34	Has anyone done the math on the price per base one would get with a 2x150bp run on the MiSeq and the HiSeq, taking into account library prep costs? People working medium-sized genomes (10-100 MBp) sometimes spend a lot of time and effort getting clean clonal DNA, so doing a try on the MiSeq would be great for them, but maybe they can wait to do 1 lane on the HiSeq if there is not much price difference...

01-28-2011, 05:46 AM	#38
genlyai Member Location: Boston, MA Join Date: Aug 2009 Posts: 39	The price per base difference will vastly favor HiSeq, but I'm not sure that's the metric you would care about if you want to quickly test the quality of your library & DNA. Wouldn't you just care about turn-around time and cost per run?

02-16-2011, 04:10 AM	#39
vebaev Senior Res. Location: Plovdiv, Bulgaria Join Date: Oct 2008 Posts: 110	Hi, our lab have used only sequencing services for mRNA-seq and smallRNAs seq with Illumina GA (for plant samples). We are quite interesting to get MiSeq since we do not have sequencer, is there any limitations that MiSeq have that we have to know before buying it? Thanks

02-19-2011, 02:09 AM	#40
vebaev Senior Res. Location: Plovdiv, Bulgaria Join Date: Oct 2008 Posts: 110	Since the covarage of MiSeq will be smaller than GA is it possible to use it for sequencing of transcriptomes (mRNA-seq, plant species in my case)? If not whole transcriptome is it possible to catch at least most abundant transcripts? The same for genome sequencing? is it possible to catch part of the genome with Miseq (again plant genome) and If needed to make more runs for more covarage of the genome? Thanks!