tag:blogger.com,1999:blog-36768584.post127740096145957603..comments2024-03-03T18:49:34.382-05:00Comments on Omics! Omics!: 2012: Enter the Nanopores?Keith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger7125tag:blogger.com,1999:blog-36768584.post-71334511757648570162012-02-16T01:29:27.022-05:002012-02-16T01:29:27.022-05:00PEOPLE!!!!
NOW HERE THIS:
Accuracy at less than ...PEOPLE!!!!<br /><br />NOW HERE THIS:<br /><br />Accuracy at less than 80% is useless for any kind of sequencing that would be used for diagnostics regardless of readlength or coverage....WHY YOU ASK? Well, if you calculate the amount of computational power and time required to gain any useful information you would be running all of IBM's machines for 2 centuries before you got any meaningful information....ASK any bioinformatician to do the calculation for you...ONT is theoretically prohibited from sequencing with an accuracy better than PacbioAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-86831244839052220942012-02-09T07:26:21.365-05:002012-02-09T07:26:21.365-05:00Hi all,
CTO of ONT here. Looking forwards to next...Hi all,<br /><br />CTO of ONT here. Looking forwards to next week and i will clarify a lot of the speculation here. One thing I cannot let pass right now is the following comment :<br /><br />"OxNano's paper at AGBT is reportedly on 'sequencing a strand'.<br /><br />That is NOT what the title says. "Strand" sequencing is in fact the generic name given to passing strand(s) of DNA through a nanopore and reading them as contrasted with, say, "exo" sequencing where bases are chopped and dropped.<br /><br />c.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-71318682482279271802012-02-07T23:14:26.698-05:002012-02-07T23:14:26.698-05:00Interesting article. I am currently doing my PhD o...Interesting article. I am currently doing my PhD on solid state nanopores and their application to single molecule detection and analysis. While I have not worked with DNA too much, I do know that such platforms also have other potential applications such as studying protein folding and even in ultra fine nanoparticle separation. <br /><br />-AnmivAnmivhttp://anmiv.wordpress.com/noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-85283864126871220182012-02-07T06:21:05.104-05:002012-02-07T06:21:05.104-05:00Anon: I forgot to put this in the original post, b...Anon: I forgot to put this in the original post, but the strand sequencing is unpartnered -- Illumina will benefit indirectly as an investor, but at the moment has no more stake than that.Keith Robisonhttps://www.blogger.com/profile/04765318239070312590noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-5717818678718772812012-02-07T02:13:33.822-05:002012-02-07T02:13:33.822-05:00OxNano will certainly use biological nanopores. Y...OxNano will certainly use biological nanopores. You don't speculate on how much multiplexing one can get out of a single rack, and my guess is "not much". Making these at the right density and addressing them individually is certainly going to be difficult... and expensive. Sure, each rack is small and compact, but if it reads a few hundred cells then you end up in the same ballpark as all other existing tools. <br /><br />Synthetic nanopores can change all that, but as a semiconductor gearhead I can assure you with absolute certainty that there is no current technology that can handle the size requirements with anything approaching commercial feasibility. This is particularly true about the membrane thickness required to achieve single-base resolution.<br /><br />OxNano's paper at AGBT is reportedly on "sequencing a strand". I would expect exquisite read lengths and single-strand error rate better than PacBio, which I am guessing is limited by the readout. As far as data throughput is concerned my prediction is that this is going to be a total "meh" moment, far behind what even PacBio can do today, and not even on the same planet and Illumina.<br /><br />Overall this will be yet another niche technology. If respectable it may be deadly to PacBio but probably for reasons that are yet to emerge.GroovyGeekhttps://www.blogger.com/profile/02461907290773954635noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-19495218242767761722012-02-07T01:14:44.114-05:002012-02-07T01:14:44.114-05:00The first line of your post says it all: it's ...The first line of your post says it all: it's been 20 years. And now the pressure to release something, anything, is all coming from Illumina who need a riposte to LifeTech's Proton, not in capability but as a statement to show they're still in the game of pushing technology. I agree PacBio should be (more) worried.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-83417158047566348242012-02-07T00:18:51.868-05:002012-02-07T00:18:51.868-05:00I suspect that they are not at the point of single...I suspect that they are not at the point of single-base resolution yet, so reads will be very noisy. Long reads may be possible though, and I understand that considerable progress is being made both in terms of controlling the movement of the DNA through the nanopore and in the precision of the reads.Kevinhttps://www.blogger.com/profile/14528751349030084532noreply@blogger.com