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Thread | Thread Starter | Forum | Replies | Last Post |
Illumina Nextra prep without using Illumina reagents | crsimao | Illumina/Solexa | 4 | 04-14-2015 10:29 AM |
Comparison between SOLiD, Illumina MiSeq and Illumina HiSeq | NGS_New_User | SOLiD | 0 | 12-12-2012 11:37 AM |
bowtie command line for Illumina Hiseq 2000 with Illumina 1.5+ quality encoding files | rworthi | Illumina/Solexa | 4 | 09-28-2011 11:25 AM |
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#1 |
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Location: East Coast USA Join Date: Feb 2008
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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. Last edited by GenoMax; 01-24-2017 at 09:05 AM. |
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#2 |
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With Novaseq now on the market, who is still going to buy HiSeq 2500/3000/4000/X?
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#3 |
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Location: genohub.com Join Date: Mar 2013
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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/ |
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#4 |
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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. |
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#5 | |
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#6 |
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#7 |
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@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. |
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#8 | |
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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. Last edited by kmcarr; 01-10-2017 at 05:15 AM. Reason: Clarification |
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#9 | |||
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With AGBT so close, it remains to be seen if we will see another major announcement there. Quote:
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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. Last edited by GenoMax; 01-10-2017 at 05:34 AM. |
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#10 |
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@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. Last edited by GenoMax; 01-10-2017 at 05:35 AM. |
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#11 |
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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.
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#12 |
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Location: Washington, D.C. metro area Join Date: Feb 2010
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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.
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#13 | ||
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Last edited by GenoMax; 01-10-2017 at 08:37 AM. |
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#14 | |
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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. |
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#15 |
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The specsheet lists 4 wavelengths.
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#16 | |
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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 IIIbso I'm not sure what the 780 and 790nm wavelengths on the NovaSeq might be used for... |
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#17 |
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the announcement from the JP Morgan Healthcare conferene on GenomeWeb describes the NovaSeq as using the two color chemistry
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#18 |
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" .... 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? |
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#19 |
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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. |
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#20 | |
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UPDATE: I just got an official, in person confirmation from two Illumina FAS's, the NovaSeq is TWO color chemistry. Last edited by kmcarr; 01-10-2017 at 11:23 AM. Reason: Breaking news |
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illumina, novaseq |
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