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Old 05-18-2011, 10:43 AM   #8
wraithnot
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Location: SF bay area

Join Date: Apr 2009
Posts: 12
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We're also trying to decide between these two instruments. I think most of the information you're after can be found here:
http://www.thestreet.com/story/10970...ng-system.html
http://www.illumina.com/systems/mise...workflow_specs
http://www.iontorrent.com/lib/images...rmation%20.pdf
http://www.iontorrent.com/lib/images...ote_041211.pdf

The last link shows actual data for the PGM "314" chip, but it looks like the performance characteristics for their other chips are estimates/speculation. If the PGM of today doesn't meet your needs, you'll need to do a bit of speculation of your own to decide how the two instruments will match up when you plan to actually buy one.

Quote:
Originally Posted by aleferna View Post
So I attended an Illumina conference, 2 weeks ago and of course I asked the obvious question... how is MiSeq better than PGM?
The answer was not as clear/black and white as I wanted, they said
1. PGM has lower quality, lots of Q20 bases??
2. Unproven technology
3. No Paired End sequencing

Well, other except for the PE, the other answers were kind of ambiguous. I'm trying to compile a comparison between the 2 devices as we are probably going to buy one of these machines next year. It would be nice to have the following raster:
1. Throughput/Hands On Time/Running Time per run
2. Quality of base 25, 50, 75, 100
3. Cost:
Equipment (PGM $50k, MiSeq $150k??)
Cost per run?
Cost per sample prep? (they said $750 for the MiSeq sequencing run, but didn't mention the sample prep.
4. Read length ?
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