Any NovaSeq user threads/sites out there?

misterc · 06-12-2018, 10:08 AM

Hi all,

With NovaSeq now 1 year old as a shipping platform, I'm curious if/where folks might be discussing their experiences with their NovaSeqs. Anything out there? I'm surprised there's little on this forum about them.

Thanks,
Charles

GenoMax · 06-12-2018, 07:19 PM

Is there something specific you want to discuss? NovaSeq works fine and is a workhorse. People in the lab like it since there is much less fuss with reagents etc. S4 FC's produce a ton of data. ~10B reads. We have tested correlation of same libraries run on NovaSeq and HiSeq 2500. No problems or odd results.

Markiyan · 06-13-2018, 03:14 AM

Dear GenoMax,

How does the quality (raw error rates) of the 2x150 runs compare with nextseq 500 2x150?

Are they quite similar given the 2 channel imaging?
And averaging 0.5%-2% errors per 2x150bp read like it is in the case of the nextseq 500?

And the frequency of the systematic errors (like oligo G tails/etc) - is it similar to nextseq 500?

GenoMax · 06-13-2018, 06:03 AM

We don't have a NextSeq in house so we have not done direct comparisons but as I understand it there are differences in NovaSeq chemistry (for better) compared to NextSeq (hard to find concrete info because of proprietary nature of these things). Spatial separation of signals is supposed to be much better in NovaSeq compared to NextSeq. Basecalls are of similar quality as HiSeq.

misterc · 06-13-2018, 09:49 AM

I'm curious if anyone else has had issues with chipped glass wreaking havoc (instrument causes this with the FC loading mechanism being too forceful, and vacuum sucks these bits of glass into the vacuum trace). We've run >200 S2 flow cells and maybe 20 S4's, so maybe the problem is more tied to S2 use with the different flow cell + bare glass setup...

GenoMax · 06-13-2018, 12:41 PM

Good to know. We have a comparatively new machine and have not used it a lot. S4 costs add up quickly, though you do get a ton of data.

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06-12-2018, 10:08 AM	#1
misterc Member Location: Livermore, CA Join Date: Jan 2016 Posts: 44	Any NovaSeq user threads/sites out there? Hi all, With NovaSeq now 1 year old as a shipping platform, I'm curious if/where folks might be discussing their experiences with their NovaSeqs. Anything out there? I'm surprised there's little on this forum about them. Thanks, Charles

06-13-2018, 03:14 AM	#3
Markiyan Senior Member Location: Cambridge Join Date: Sep 2010 Posts: 116	Novaseq ws Nextseq 500? Dear GenoMax, How does the quality (raw error rates) of the 2x150 runs compare with nextseq 500 2x150? Are they quite similar given the 2 channel imaging? And averaging 0.5%-2% errors per 2x150bp read like it is in the case of the nextseq 500? And the frequency of the systematic errors (like oligo G tails/etc) - is it similar to nextseq 500?

06-12-2018, 07:19 PM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Is there something specific you want to discuss? NovaSeq works fine and is a workhorse. People in the lab like it since there is much less fuss with reagents etc. S4 FC's produce a ton of data. ~10B reads. We have tested correlation of same libraries run on NovaSeq and HiSeq 2500. No problems or odd results.

06-13-2018, 06:03 AM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	We don't have a NextSeq in house so we have not done direct comparisons but as I understand it there are differences in NovaSeq chemistry (for better) compared to NextSeq (hard to find concrete info because of proprietary nature of these things). Spatial separation of signals is supposed to be much better in NovaSeq compared to NextSeq. Basecalls are of similar quality as HiSeq.

06-13-2018, 09:49 AM	#5
misterc Member Location: Livermore, CA Join Date: Jan 2016 Posts: 44	I'm curious if anyone else has had issues with chipped glass wreaking havoc (instrument causes this with the FC loading mechanism being too forceful, and vacuum sucks these bits of glass into the vacuum trace). We've run >200 S2 flow cells and maybe 20 S4's, so maybe the problem is more tied to S2 use with the different flow cell + bare glass setup...

06-13-2018, 12:41 PM	#6
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Good to know. We have a comparatively new machine and have not used it a lot. S4 costs add up quickly, though you do get a ton of data.