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Old 02-25-2012, 03:14 PM   #36
Location: Pacific Northwest

Join Date: Oct 2010
Posts: 52

Originally Posted by clivey View Post
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.
Let me clarify that I appreciate the speed and asynchronous nature of the readout very much, and perhaps by continuously nitpicking on paralelism I am leaving the wrong impression of how I view ONT's announcement. The whole technology is rather impressive sounding, even if (probably) somewhat puffed up for presentation reasons :smile:

However, there are certain applications where parallelism matters and others where long reads do. The trivial example is a 100-page book that is read "competitively" by 100 people reading 1 pg/min and 1 person reading 50 pg/min. If you want the contents of the whole book you definitely want the latter, it will be much easier to piece the storyline together. However, if you want the contents of a single page the former is preferable. This is something that pretty much everyone on Seqanswers appreciates.

Things get a bit more interesting when you increase the size of the book, throw in errors, and introduce a random selection of segments. If you are interested in a certain short stretch of pages the statistical advantage of massively parallel short & slow reads becomes considerable. It is my understanding that this is what clinical applications are all about, and this was the context in which I made my latest remark. Several people have already stated that if ONT's technology is anywhere close to what was presented it is likely to thrive by creating its own niches of new applications. However, displacing short-reads does not seem to be one of them.

Originally Posted by clivey View Post
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.
Absolutely. Both = throughput, and for many applications this is all that matters. Walmart makes a ton of money over billions of transactions where they make a few cents on each. Oracle makes its money by making thousands of dollars on thousands of transactions.

However, for certain applications the metrics are different, and this is where I find ONT's "run until" marketing a bit over the top. If you are after only a certain information then the error of the read can matter, and long reads on a randomly cleaved strand can be a disadvantage when the accuracy is <100%.

Originally Posted by clivey View Post
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.
This is not inherent, but a characteristic of the particular sensor technology. I suspect that you are referring to nanopore technology specifically.

In any case, thanks for taking the time to write. Your presence in these debates is much appreciated, and very different from the approach other companies are using.
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