tag:blogger.com,1999:blog-36768584.post1472428467869217886..comments2024-03-03T18:49:34.382-05:00Comments on Omics! Omics!: ONT Updates: GridION X5, PromethION, 1D^2, Scrappie, FPGAs and MoreKeith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger32125tag:blogger.com,1999:blog-36768584.post-75118715761101904482017-06-21T18:00:42.131-04:002017-06-21T18:00:42.131-04:00So, how are their sales in comparison to PacBio? A...So, how are their sales in comparison to PacBio? Are they catching up?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-61918043591866427852017-05-02T21:30:15.622-04:002017-05-02T21:30:15.622-04:00More details on the GridION. CapEx. You only get 1...More details on the GridION. CapEx. You only get 18month discount. OpEx you have to use 300 flow cells in 12 months that is about ~60% of capacity assuming 5 day work week and 50 weeks. <br /><br />It hard to look at the GridION as anything but a massive service provider fee that doesn't go away. What happens in year 2? do I have to buy another 300?<br /><br />With MinION I could buy 5 for 5k (assuming ONT would sell them to us) and a 48 pack to. That would get us to a $500 discount level for a total of 29k vs 157k for OpEx (300 X 475)+ 14999 service contract))Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-31934532269758591222017-03-30T04:58:31.493-04:002017-03-30T04:58:31.493-04:00Thanks Ben for your quick reply.
I think PacBio ...Thanks Ben for your quick reply. <br /><br />I think PacBio still has an edge when very high base accuracy is required. Also, PacBio's methylation stuff is at production level whereas ONT remains research grade.<br /><br />I would not say is doomed on a science level as long as they can still crave out a big enough niche to keep them survive commercially. <br /><br />I think ONT's technology depends heavily on the protein they use to make the pores. In this R9 generation, they managed to improve accuracy and throughput significantly such that PacBio's niche is further reduced.<br /><br />The problem of ONT is they need to find new protein that makes better pores. This is more a hit-and-miss process. On the other hand, PacBio's progress can be more steady as it depends more on advances in optics and compute.<br /><br />ONT claims they have an new R10 protein. Let's wait and see what it brings. I hope PacBio can also come up with something even better soon. I think most scientists would rather PacBio stay long to serve as an alternative and a competitor to ONT.<br /><br />Geneticist from the Eastnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-62629775520707600902017-03-29T15:29:01.601-04:002017-03-29T15:29:01.601-04:00Isn't CCS essentially just coverage though, bu...Isn't CCS essentially just coverage though, but in a form with a vastly lower read length?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-77061074062883192162017-03-29T00:01:00.854-04:002017-03-29T00:01:00.854-04:00Here is the coverage data on Sequel: (~5x coverag...Here is the coverage data on Sequel: (~5x coverage needed for QV20)<br />http://www.pacb.com/smrt-science/smrt-sequencing/accuracy/<br /><br />If you use their CCS method you only need 2x coverage:<br />https://www.omicsonline.org/articles-images/data-mining-genomics-Read-quality-value-4-136-g003.png<br /><br />The recent human sequencing effort with minion showed ~30x coverage to get 99% (Qv20) accuracy:<br />https://genomeinformatics.github.io/NA12878-nanopore-assembly/<br /><br />Hope that helps. <br /><br /><br /><br />Bennoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-51893380035553828962017-03-26T23:24:39.259-04:002017-03-26T23:24:39.259-04:00Hi Ben,
Are there any paper or preprint that ...Hi Ben,<br /><br /> Are there any paper or preprint that shows how much coverage is needed for Sequel and R9.4 to achieve QV20? Thanks a lot in advance.<br /><br />Geneticist from the Eastnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-29151891645480429822017-03-24T06:21:34.355-04:002017-03-24T06:21:34.355-04:00Not a paid commentator at all, nor am I a consulta...Not a paid commentator at all, nor am I a consultant in any way. I admit that as a Brit I am heavily biased, however.<br /><br />I am also bored of the same old, same old SBS though. Nanopore is a fundamentally different approach and that is refreshing. I also think that is the reason PacBio can't and doesn't compete on a science level.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-64565934318416234472017-03-23T10:40:51.655-04:002017-03-23T10:40:51.655-04:00@Ben, unfortunately it appears you are making your...@Ben, unfortunately it appears you are making your case to someone who appears to be paid to make these comments - At least I would be skeptical of someone who scripts comments with lines such as 'You make a fair point and 'on a science level...' <br /><br />In spite of Keith's best intentions, the comments section can be a bit of an echo chamber and if you are arguing with an active paid commentator who is not actively involved in the tech and whose sole purpose is to make sure ONT always looks good, there is very little actually learning from the discussions in comments.<br /><br />One way to improve this is to make commenting truly non-anonymous but that comes with its own pitfalls.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-54301284543070677722017-03-21T17:07:13.427-04:002017-03-21T17:07:13.427-04:00I'm actually confident they can reach 32x by t...I'm actually confident they can reach 32x by the end of next year. Pacbio increased the throughput of the RS by about 100x over 4 years and I'm sure they can continue that on the Sequel. Their technical team is top notch. It's the management team that seems to be lagging. It's a shame because what they have accomplished technically is amazing. Too bad their management team has been making poor decisions (with this new patent lawsuit being the most recent). I can't believe Mike H. actually thinks they could win this case. What a waste of money for everyone. Maybe the board will get rid of him. He lost the Roche deal and now he's spending resources on patent trolling lawsuits. What a joke. Bennoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-11848851453289115552017-03-21T12:56:20.186-04:002017-03-21T12:56:20.186-04:00Ah ok, thanks for clarifying.
I guess it will be...Ah ok, thanks for clarifying. <br /><br />I guess it will be interesting to see how fast each progress. Sequel seems like the only major upgrade PacBio has done in 6yrs so not sure I'm convinced by their claim of a further 32x in 20 months.<br />Contrast that with the 20 month lifespan of MinION where they have managed to get higher throughput than a Sequel on something that is actually Lego size already (although as you contest throughput isn't everything). It has also done it with reads of nearly 1 Mb in length.<br /><br />I guess I just hope it is the end of fluorescence, based on a love-hate relationship of growing up with it, haha.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-45487627373233643942017-03-21T12:02:40.883-04:002017-03-21T12:02:40.883-04:00I don't believe company specs. A fair compari...I don't believe company specs. A fair comparison is Pacbio customers get ~5-8GB/run while ONT customers get 1-10GB/run. So far no customer of ONT are getting 20GB. That's an upgrade planned for the future. But Pacbio also said they are increasing the throughput to 20GB/run this year. Until customers actually start getting those values there's no point of claiming that's what the technology can product. We need to compare what customers are getting now. <br /><br />I believe the 15x QV20 ONT data was provided by ONT about their updated basecaller. I don't think any customer has produced that. Even if it's true that still means you need 3x more ONT data to produce a similar quality genome as Pacbio. <br /><br />I think the lego toys ended up being a big hit at AGBT. But it's not like that will sell them more instruments. Management seems to handle major decisions pretty poorly. Bennoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-5299934129012189122017-03-21T07:04:53.907-04:002017-03-21T07:04:53.907-04:00"Your comparison isn't apples to apples. ..."Your comparison isn't apples to apples. With current ONT 9.4 and basecalling methods it takes roughly 30x coverage to reach QV20. It only takes 5x coverage of pacbio sequencing to reach QV20. And if your using Pacbio CCS you hit >QV20 with just 2 passes. So if you're looking to assemble a 1GB genome with QV20 you would need 30GB of nanopore data or 5GB of pacbio data."<br /><br />You make a very fair point, although I thought the latest data releases showed 15x was required for QV20 with MinIon (I will try to dig out where i saw that - I think Jared Simpson but please say if anyone knows to save me effort haha)? With that in mind and if you believe company specs (again haha); PacBio claim sequel is 9 GB and Nanopore 20 GB. Therefore I stand by my point that on a science level the Sequel just can't compete (again there is also cost and practical considerations that work against Sequel). <br /><br />A side point but why do PacBio make Lego toys, surely it just illustrates what a behemoth the Sequel is!? Their PR department need sacking for that as they look stupid when their competitor is actually tiny (gimmicks irritate me but badly thought out gimmicks... urgh)?! Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-46873008055181292852017-03-20T21:32:46.901-04:002017-03-20T21:32:46.901-04:00To the poster above me:
Your comparison isn't...To the poster above me:<br /><br />Your comparison isn't apples to apples. With current ONT 9.4 and basecalling methods it takes roughly 30x coverage to reach QV20. It only takes 5x coverage of pacbio sequencing to reach QV20. And if your using Pacbio CCS you hit >QV20 with just 2 passes. So if you're looking to assemble a 1GB genome with QV20 you would need 30GB of nanopore data or 5GB of pacbio data. Just looking at raw output without looking at error rates is useless when pricing the cost of a genome. This is why pacbio still dominated the long read market and (currently) ONT is not more cost effective. Both companies claim major upgrades in the next year so we will have to wait and see how it plays out. <br /><br />On the other hand I agree with you about the patent trolling. I really wonder what's going on in the mind of pacbio execs. It seems like the past few months have been filled with poor decisions (including losing the roche contract). Maybe they are using these patents to increase the company value for a sale. Bennoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-54927433757188401072017-03-20T18:35:38.015-04:002017-03-20T18:35:38.015-04:00I saw Alexander Wittenberg's tweet about the S...I saw Alexander Wittenberg's tweet about the Sequel only managing 5-6 GB and then Nick Loman's tweet, almost the next day, of a 5 GB Minion run that had 800kb reads in it. That's hard for PacBio to compete with on a science level. Couple that with the fact that anyone with $1000 can do it, not just facilities that can stump up $350k and the required space for a Sequel, then we can all see the writings on the wall. I know PacBio promise there will be 32x more throughput by the end of 2018 but that is in 20 months time, look at what Nanopore have done in the last 20months, how far ahead they will be by then?<br /><br />To take an action that could be said to have a whiff of patent trolling indicates to me time is short and they are desperate. Will they be here in 20 months to deliver 32x?<br />That makes the logic of a district court action seem odd as they take years to conclude, by which time PacBio will likely be long gone.<br /><br />My guess is they know times is short and their only option to save themselves is an acquisition. They can't appeal to Roche or Illumina with their product (remember Roche dumped them) but they can try to make out that buying them offers the buyer a Nanopore torpedo.<br /><br />That is my guess anyway.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-36427504038607883082017-03-20T17:24:55.290-04:002017-03-20T17:24:55.290-04:00"PacBio's "sequencing with nanopore ..."PacBio's "sequencing with nanopore using n-mers" is really strange. They are claiming the same stuff that Clive showed in the original minIon unveiling slides and this was filed 3 years after that.<br /><br />The patent it extends from 2010 looks like a basic, general description of nanopore sequencing that was already covered by patents from the 90s. How were they awarded any of these?! I'd love to hear from someone better informed."<br /><br />The USPTO is very sloppy. It allows things through that other patent authorities don't, then they are settled in expensive lawsuits. Almost like a tax on doing business in the US. For example, EU PTO an Japan have stronger filters on patent allowance upfront. The patents in question have not been enabled by Pacbio and are concepts, the key claims were appended following ONTs AGBT 2012 talk. People can draw their own conclusions about the fairness of that. My reading is that ONT don't practice any of the patents Pacbio is suing them on anyway. It is likely therefore that either Pacbio don't understand the technology, or are resorting to litigation as a fig leaf, knowing full well they are rolling dice.<br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-44070939382451022462017-03-20T15:52:20.969-04:002017-03-20T15:52:20.969-04:00PacBio's "sequencing with nanopore using ...PacBio's "sequencing with nanopore using n-mers" is really strange. They are claiming the same stuff that Clive showed in the original minIon unveiling slides and this was filed 3 years after that.<br /><br />The patent it extends from 2010 looks like a basic, general description of nanopore sequencing that was already covered by patents from the 90s. How were they awarded any of these?! I'd love to hear from someone better informed.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-16283104816304889672017-03-19T13:03:53.577-04:002017-03-19T13:03:53.577-04:00Surely it's more throughput than miseq. Though...Surely it's more throughput than miseq. Thought miseq was 15-20G in 24 hrs ? The recent MinION runs were 20G in 48 each. They're claiming to double that again soon. So surely 5 of them is ~= 2 miseqs ? This also ignores sample prep time, quick on nanopore. What's in a miseq ? A camera and a pump and a PC and glass flowcells.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-18641398073893999272017-03-19T01:30:30.684-04:002017-03-19T01:30:30.684-04:00No, it is very common actually. Just google "...No, it is very common actually. Just google "patent troll".Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-4606911543858743922017-03-18T21:13:55.766-04:002017-03-18T21:13:55.766-04:00Will you be writing a post about the "sequenc...Will you be writing a post about the "sequencing with nanopore using n-mers" patent that pacbio was awarded? I'm really curious to read your analysis on this one! It's pretty crazy that a company who doesn't even use nanopores managed to jump on the patent before anyone else. <br /><br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-20637169669761150212017-03-15T18:19:40.046-04:002017-03-15T18:19:40.046-04:00So 5 minions at $1000 or less each equals one X5 a...So 5 minions at $1000 or less each equals one X5 at $125k. Sure there is some compute cost in the GI but $120k? Surprised that there has not been more chatter about this. When you compare apples to apples (ie Q30 data) a GI costs slightly more than a Miseq and produces about the same output in 3x the time (assuming an optimistic 20G per flowcell in 60 hrs and 20 fold coverage required to reach Q30). Hmm... Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-23219080797291231162017-03-15T15:53:35.126-04:002017-03-15T15:53:35.126-04:00Lars,
Thanks -- will update! Wish they had been ...Lars,<br /><br />Thanks -- will update! Wish they had been explicit like that on the slides.Keith Robisonhttps://www.blogger.com/profile/04765318239070312590noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-33374602364817063282017-03-15T15:41:50.373-04:002017-03-15T15:41:50.373-04:00I read that as 'using existing MinION flow cel...I read that as 'using existing MinION flow cell design'. The products page explicitly says "Use up to five MinION Flow Cells at a time" https://nanoporetech.com/productsAnonymoushttps://www.blogger.com/profile/12369203735107346437noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-46907810680320874962017-03-15T15:25:09.049-04:002017-03-15T15:25:09.049-04:00Lars,
That's my inference; I could be wrong (...Lars,<br /><br />That's my inference; I could be wrong (I should check with ONT). Clive's slide says "Based on on current MInION flowcell design", which I took to mean they are not MinION flowcells. But perhaps someone just chose odd wording on the slideKeith Robisonhttps://www.blogger.com/profile/04765318239070312590noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-90607532247444739152017-03-15T14:59:42.467-04:002017-03-15T14:59:42.467-04:00Where does the information about MinION/GridION fl...Where does the information about MinION/GridION flowcells not being compatible come from?Anonymoushttps://www.blogger.com/profile/12369203735107346437noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-8258764660011802202017-03-15T11:08:33.220-04:002017-03-15T11:08:33.220-04:00Albert Vilella has looked at my chart and he sugge...Albert Vilella has looked at my chart and he suggested that the CapEx might include for free the first 300 flowcells<br /><br />so the price would remain fixed up to 300 flowcells then the flowcells would cost 299 up to the 750 flowcell purchased (300+450) and then revert to 475 for the remaining ones<br /><br />This would make the CapEx much more atractive<br /><br />https://docs.google.com/spreadsheets/d/1YpKZp9WP8YmNaBfYtpklulQJCdLH6XcmJ_XzR9zMdls/pubchart?oid=522361220&format=interactive<br />Duartehttps://www.blogger.com/profile/13960784528179885911noreply@blogger.com