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Old 05-04-2017, 02:53 AM   #1
WhatsOEver
Senior Member
 
Location: Germany

Join Date: Apr 2012
Posts: 215
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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