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Old 02-24-2012, 11:31 PM   #32
Location: Oxford

Join Date: Jul 2008
Posts: 24

BBoy. You weren't at the talk so I will clairy if I can.

You raise the point about parallelism a lot. What you fail to consider is speed. Not all sensing circuits are the same. On a Nanopore system, the chemistry is not cyclical and not synchronized, its free running. How many bases per second you can measure depends on how quickly you can read the channel and at what noise. 8k channels at 1000 bases per second per channel is in fact more data than a million sensors at 1 base per second per channel (obviously). Not all chips or circuits are the same. And there are significant constraints on the kinds of circuits you can pack onto silicon without making trade offs in speed and noise. Theres the rub in terms of sensor design. If your noise is too high, at the given sample rate, you won't be sequencing. One answer proposed elsewhere for this is to "floss" DNA and read it several times. Good, but of course if you read it 4 times that's then like running 1/4 the number of sensors once in terms of throughput.

So with a Nanopore systems parallelism is only half the story -- speed (and signal to noise at that speed) are the other. Both are important, not just the parallelism. A sensor needs to be judged on both.

The other important and often overlooked feature is sensor lifetime. Small volume wells or bubbles won't last very long. Minutes or hours. You won't get much data from that. Larger volume systems run for longer and give more data per chip, lowering cost per base.

Any of the rules that apply to cyclical chemistries, like density of features, are not quite the same on a real time system. Nanopore systems are very different.

Last edited by clivey; 02-25-2012 at 01:16 AM. Reason: Clearer wording
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