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Old 05-04-2017, 01:53 AM   #1
WhatsOEver
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Default Pacbio sequel for single cell human WGS?

Hi @all,
we are currently struggling with pros/cons of buying a PB sequel vs ONT Promethion for our analyses (human de novo single celll WGS). Ideally we are looking for something with which we can analyse structural variants and SNPs (so something with ~100Gb+ (>30x) output).
Unfortunately, we're getting extremely diverse information about the specifications of the two systems. Hence, I'd like to ask users of each system for info on their experience (I have therefore a similar post in the ONT forum).

My information on the sequel so far:
1) Accuracy of >99.999%
Is this a consensus acc from assembly/mapping? As this would be coverage dependent, it is meaningless for me... What about individual read (CCS) accuracy? I know there is something mentioned on the PB website, but I don't really understand their graph http://www.pacb.com/smrt-science/smr...cing/accuracy/

2) Output of ~5Gb per SMRT cell / ~800 per SMRT cell run
So, I would need ~20 SMRT cells / genome => ~16k / genome? However, I have heard from colleagues who tested the system that a cost of 30-40k / genome would be more realistic for our aims?!

3) Price ~350k
Is installation, training, etc. included? Or any consumables?

4) Waiting for deliverables
Some colleagues told us that they are waiting sometimes for month to get deliverables (esp. chips seem to be a problem)

I would be grateful for any information on any of my four points.
Thanks!
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Old 05-09-2017, 10:27 AM   #2
Bukowski
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1) Accuracy of >99.999%

- Yes this will be consensus accuracy at depth.

2) Output of ~5Gb per SMRT cell / ~800 per SMRT cell run

- That's about what we're seeing. Without going too far into pricing, the costs are going to be much higher per cell/run with consumables, labour etc.

3) Price ~350k
Is installation, training, etc. included? Or any consumables?

- Yes, yes, no.


4) Waiting for deliverables

- We have never had issues with consumable deliveries.
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Old 05-09-2017, 11:49 PM   #3
WhatsOEver
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Quote:
Originally Posted by Bukowski View Post
2) Output of ~5Gb per SMRT cell / ~800 per SMRT cell run

- That's about what we're seeing. Without going too far into pricing, the costs are going to be much higher per cell/run with consumables, labour etc.
Thanks a lot for your input @Bukowski. Could you just very briefly elaborate what "much higher" means here - should we expect 1k? 2k? More?
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Old 05-09-2017, 11:56 PM   #4
Bukowski
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Quote:
Originally Posted by WhatsOEver View Post
Thanks a lot for your input @Bukowski. Could you just very briefly elaborate what "much higher" means here - should we expect 1k? 2k? More?
The Sequel consumables starter kit, which provides enough materials for 16 cells is 20k - admittedly this is not the cheapest way to buy consumables, but is closer to 1.25k/cell.
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Old 06-23-2017, 04:15 PM   #5
weigrc
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Quote:
Originally Posted by Bukowski View Post

4) Waiting for deliverables

- We have never had issues with consumable deliveries.
SMRT cell delivery schedule is ok, but its shelf-life, usually 1-2 months left after arrived. And although SMRT cells is 4 per tray for purchase, but the sequencing kit is one plate for 8 cells, allowing few days to use up the sequencing kit once opened.
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Old 06-27-2017, 11:02 AM   #6
Brian Bushnell
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Quote:
Originally Posted by WhatsOEver View Post
My information on the sequel so far:
1) Accuracy of >99.999%
Is this a consensus acc from assembly/mapping? As this would be coverage dependent, it is meaningless for me... What about individual read (CCS) accuracy? I know there is something mentioned on the PB website, but I don't really understand their graph http://www.pacb.com/smrt-science/smr...cing/accuracy/
The graph indicates that the more coverage you have, the higher the quality of the self-corrected data (meaning reads corrected by other reads in the same library, not reads corrected by themselves). Last I saw, our RSII was producing 86-87% accurate reads and Sequel was producing 80-83% accurate reads, according to PacBio's software. CCS accuracy simply depends on how long the movie is compared to the insert size; for long insert libraries that you would generate for SV's, you would not yield many useful multi-pass CCS reads.
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