Lotsa new toys from Illumina: HiSeq X Five, 3000, 4000, NextSeq 550

GW_OK · 01-12-2015, 11:36 AM

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

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

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

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

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

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

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.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
A first look at Illumina’s new NextSeq 500	AllSeq	Vendor Forum	111	03-12-2020 03:25 AM
NextSeq 500 and HiSeq X Ten Services Coming Soon to Genohub.com	Genohub	Vendor Forum	11	04-22-2014 09:46 AM
Comparison between SOLiD, Illumina MiSeq and Illumina HiSeq	NGS_New_User	SOLiD	0	12-12-2012 12:37 PM
bowtie command line for Illumina Hiseq 2000 with Illumina 1.5+ quality encoding files	rworthi	Illumina/Solexa	4	09-28-2011 12:25 PM
Have someone use the Misonix 4000 for solexa	allwayscjh	Sample Prep / Library Generation	0	12-07-2010 02:05 AM

01-12-2015, 11:36 AM	#1
GW_OK Senior Member Location: Oklahoma Join Date: Sep 2009 Posts: 411	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

01-12-2015, 02:52 PM	#10
SNPsaurus Registered Vendor Location: Eugene, OR Join Date: May 2013 Posts: 521	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). __________________ Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

01-12-2015, 03:35 PM	#12
SNPsaurus Registered Vendor Location: Eugene, OR Join Date: May 2013 Posts: 521	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. __________________ Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

01-13-2015, 10:18 PM	#20
SNPsaurus Registered Vendor Location: Eugene, OR Join Date: May 2013 Posts: 521	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. __________________ Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

01-12-2015, 12:02 PM	#2
Brian Bushnell Super Moderator Location: Walnut Creek, CA Join Date: Jan 2014 Posts: 2,707	Any idea if the HS4000/5000 are using 4-color or 2-color chemistry?

01-12-2015, 12:09 PM	#3
GW_OK Senior Member Location: Oklahoma Join Date: Sep 2009 Posts: 411	I think that's Nextseq only? Looks to me like they've just stuck HiseqX-style flowcells in the 2500 system.

01-12-2015, 12:21 PM	#4
Brian Bushnell Super Moderator Location: Walnut Creek, CA Join Date: Jan 2014 Posts: 2,707	Except that I'm pretty sure the X-series do use 2-dye chemistry, the same as NextSeq...

01-12-2015, 01:00 PM	#8
westerman Rick Westerman Location: Purdue University, Indiana, USA Join Date: Jun 2008 Posts: 1,104	New toys for one person is a funding/migration headache for another. Especially if there is no upgrade path. :-(

01-12-2015, 02:29 PM	#9
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,358	Made the title more explicit and promoted to the front page...

01-12-2015, 03:06 PM	#11
nucacidhunter Jafar Jabbari Location: Melbourne Join Date: Jan 2013 Posts: 1,238	There are data from PCR-free, RNA-Seq and NRC libraries sequenced on HiSeq 4000 in BaseSpace.

01-13-2015, 05:56 AM	#13
HeinKey Member Location: Wageningen, Netherlands Join Date: May 2009 Posts: 21	#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...

01-13-2015, 06:23 AM	#14
kmcarr Senior Member Location: USA, Midwest Join Date: May 2008 Posts: 1,178	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.

01-13-2015, 09:57 AM	#18
FWOS Epigenomics NGS Beast Location: New Jersey Join Date: Oct 2010 Posts: 17	Pretty sure they will initially only support 2x125 in 3.5 days

01-13-2015, 08:35 PM	#19
Genohub Registered Vendor Location: genohub.com Join Date: Mar 2013 Posts: 210	"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