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  • #91
    Originally posted by AllSeq View Post
    The PGM is known for speed, decent read lengths (up to 400b) and not dealing too well with homopolymers. There's new chemistry on the horizon that might significantly improve the homopolymer issue.

    Should you get one (more or less for free)? If you highly value quick runs (<1 day instead of 24 hours) and have lots of small targeted sequencing projects, it might be a good choice to add to your panel of instruments.

    But nothing is truly free - be sure you have the time both to teach yourself how to use this new platform and to support it/keep it running.
    Thank you for your quick answer -- it's very much in line with my thinking. One of our primary concerns was about support and maintenance costs (rather than monetary costs). We do a fair amount of amplicon sequencing but our MiSeq isn't overbooked. We will likely be doing more of it in the near future, and potentially in GC-rich microbes, so the homopolymer issue was a concern too (and was one of the reasons I was turned off by the 454 data I analyzed in grad school -- too many indels -- though I realize things are always improving). Sounds like we'll really have to think this out. Do you have any references on the new chemistry? I'm all up-to-date with Illumina's R&D efforts but haven't heard much from Life. Thanks again!

    Comment


    • #92
      Happy to help. The new chemistry is called Hi-Q. An early access program for it was announced at ASHG, with a full launch expected around July this year. In theory it's already available to PGM customers (via the early access program), but I haven't heard much about it since the original announcement. You can read more about it here: http://ir.lifetechnologies.com/relea...leaseID=798937
      AllSeq - The Sequencing Marketplace
      [email protected]
      www.AllSeq.com

      Comment


      • #93
        Originally posted by AllSeq View Post
        Happy to help. The new chemistry is called Hi-Q. An early access program for it was announced at ASHG, with a full launch expected around July this year. In theory it's already available to PGM customers (via the early access program), but I haven't heard much about it since the original announcement. You can read more about it here: http://ir.lifetechnologies.com/relea...leaseID=798937
        Boom! Thanks again! I'm guessing we'll have another update come AGBT next month (unfortunately I'm on the waiting list...).

        Comment


        • #94
          Any updated answer to my question posted a year ago???

          Is Proton 2 chip a vaporware?

          Comment


          • #95
            Originally posted by ymc View Post
            Any updated answer to my question posted a year ago???

            Is Proton 2 chip a vaporware?
            Well, the latest is 'early access in early 2015'. Probably not vaporware, but definitely not the "HiSeq killer" it was supposed to be. Too little, too late.
            AllSeq - The Sequencing Marketplace
            [email protected]
            www.AllSeq.com

            Comment


            • #96
              lets see what comes new from IT on ASHG, I know Illumina will come with some more things but all of them have ben announced previously. Last thing i heard from a customer was that P2 will be around 20Gb of output so way below a killer for a Hiseq, NextSeq or a MiSeq.

              Much more interesting is the bench top from CG/BGI and whatever Quiagen will release at some point for the clinical sector but also there i have no news (maybe All Seq has?? )

              Comment


              • #97
                Originally posted by Buzz0r View Post
                Much more interesting is the bench top from CG/BGI and whatever Quiagen will release at some point for the clinical sector but also there i have no news (maybe All Seq has?? )
                Well, a desktop system from CG/BGI would certainly be news to us. CG is basically a room-sized sequencer and I haven't heard any rumors about turning it into something smaller (or even something to be sold as anything other than a service). The pyrosequencer listed in the message below is out of BIG and not BGI - is that the one you were thinking of?

                As for the Qiagen/IBS GeneReader, we've not heard much about that lately. With the push that the MiSeq and now the PGM are making into the clinic, the longer the GeneReader takes to get to the market, the harder it will be for Qiagen to win marketshare. Hopefully we'll all learn more at ASHG or AGBT.
                AllSeq - The Sequencing Marketplace
                [email protected]
                www.AllSeq.com

                Comment


                • #98
                  Originally posted by Buzz0r View Post
                  lets see what comes new from IT on ASHG, I know Illumina will come with some more things but all of them have ben announced previously. Last thing i heard from a customer was that P2 will be around 20Gb of output so way below a killer for a Hiseq, NextSeq or a MiSeq.

                  Much more interesting is the bench top from CG/BGI and whatever Quiagen will release at some point for the clinical sector but also there i have no news (maybe All Seq has?? )
                  20GB seems unlikely given the throughput of the P1 is almost there. Read number might be more interesting.

                  Qiagen has gone silent, but they went on an acquisition spree getting things lined up. It'll be interesting to see how they package it all together.

                  Comment


                  • #99
                    Originally posted by snetmcom View Post
                    20GB seems unlikely given the throughput of the P1 is almost there. Read number might be more interesting.
                    We've been hearing 20-30Gb as well. As you say, that's not that different from a PI, so not that impressive. But the hope is that it would have room to grow over time as they get longer read lengths out of the chip. (They generally have to start with only the shorter reads as noise is an issue. As they deal with the noise, longer reads become possible.)

                    Read number should be substantially higher - >300M useable reads per chip. If they hit that, the PII could be a really nice machine for 'counting' applications where shorter read length and lower quality can be better tolerated.

                    But that's still a niche and not a HiSeq-killer.
                    AllSeq - The Sequencing Marketplace
                    [email protected]
                    www.AllSeq.com

                    Comment


                    • Is there any updated comparisons between the Proton and the MiSeq?
                      Last edited by aleferna; 01-21-2015, 09:24 AM.

                      Comment


                      • Hi all!


                        My institute will purchase a benchtop sequencer for bacterial genome sequencing. It will be used both for routine genome seq and (importantly) for infetious disease outbreak analyses. Hence, although only one of many important parameters, time from DNA isolation to results is important.

                        I am positively inclined towards the MiSeq, as I have only good experience with Illumina data (HiSeq and MiSeq). However, at a presentation at the institute, they weren´t really that impressive. Ion Torrent, on the other hand sent an expert on bacterial genome sequencing, who, it seems managed to sway a lot of people.

                        I find it difficult to make a sound comparison. The published literature largely favors MiSeq for quality of sequences and throughput. However, Ion Torrent claims that the Ion 318 v2 Chip yields improved quality. And throughput isn´t necessarily that important. They also claim that library prepping is fast (<2 hrs) and automated.

                        Also, what convinced people at my institute was data handling: the Ion Torrent seems to come with built-in software that can output variant calls and that can be tailor maid for various outputs (e.g. resistance gene mutations etc). This sounds nice, but I have a feeling that this way of doing things is not very flexible…

                        Some specific questions:

                        -Has anyone experience with long read MiSeq (2x250 or so) AND Ion torrent (418 bp reads)? Any thoughts on whats best?

                        -Is mate-pair sequencing on Ion Torrent something that must be done in a separate run following «normal» single end sequencing?

                        -Even though Ion Torrent is a lot more bulky and has more steps, It seems like it is a lot faster than MiSeq long reads. Is that correct?

                        -Is it problematic doing comparative genomic analyses with data from Illumina and Ion torrent together?

                        -M. tuberculosis (65% GC content) is among the bacteria that will be sequenced routinely. Ion Torrent seems to suck at high GC but I have only found one paper on this. How much is this of a problem? Ion Torrent showcased the use of Ion Torrent for quick resistance determination in M. tuberculosis, but this scheme relied on amplicon sequencing, which in my view is a bit like walking backwards into the future……

                        Please excuse this chaotic post, but there are so many questions...

                        All feedback appreciated,

                        Vegard

                        Comment


                        • Originally posted by vehuardo View Post
                          Hi all!


                          My institute will purchase a benchtop sequencer for bacterial genome sequencing. It will be used both for routine genome seq and (importantly) for infetious disease outbreak analyses. Hence, although only one of many important parameters, time from DNA isolation to results is important.

                          I am positively inclined towards the MiSeq, as I have only good experience with Illumina data (HiSeq and MiSeq). However, at a presentation at the institute, they weren´t really that impressive. Ion Torrent, on the other hand sent an expert on bacterial genome sequencing, who, it seems managed to sway a lot of people.

                          I find it difficult to make a sound comparison. The published literature largely favors MiSeq for quality of sequences and throughput. However, Ion Torrent claims that the Ion 318 v2 Chip yields improved quality. And throughput isn´t necessarily that important. They also claim that library prepping is fast (<2 hrs) and automated.

                          Also, what convinced people at my institute was data handling: the Ion Torrent seems to come with built-in software that can output variant calls and that can be tailor maid for various outputs (e.g. resistance gene mutations etc). This sounds nice, but I have a feeling that this way of doing things is not very flexible…

                          Some specific questions:

                          -Has anyone experience with long read MiSeq (2x250 or so) AND Ion torrent (418 bp reads)? Any thoughts on whats best?

                          -Is mate-pair sequencing on Ion Torrent something that must be done in a separate run following «normal» single end sequencing?

                          -Even though Ion Torrent is a lot more bulky and has more steps, It seems like it is a lot faster than MiSeq long reads. Is that correct?

                          -Is it problematic doing comparative genomic analyses with data from Illumina and Ion torrent together?

                          -M. tuberculosis (65% GC content) is among the bacteria that will be sequenced routinely. Ion Torrent seems to suck at high GC but I have only found one paper on this. How much is this of a problem? Ion Torrent showcased the use of Ion Torrent for quick resistance determination in M. tuberculosis, but this scheme relied on amplicon sequencing, which in my view is a bit like walking backwards into the future……

                          Please excuse this chaotic post, but there are so many questions...

                          All feedback appreciated,

                          Vegard
                          Well, Illumina has PCR free kit for metagenomics. If you are serious about metagenomics, Illumina is the only way for now.

                          Comment


                          • We bought the MiSeq when the PGM came out and was still comparable with the MiSeq. I don't know about Ion, but it seems the MiSeq simply works... consistently and as advertised. I've read in other reviews the Ion prep is very tricky but I'm not sure if that still applies with their new kits and machines. I would also take into consideration that there is a chance Ion won't survive given that they have fallen behind in all their promises. There are few niche applications where the PGM is better than the MiSeq, I'm not sure if these are enough to sustain their market, make sure that you don't buy a machine that will be discontinued in a few years.

                            Comment


                            • Originally posted by aleferna View Post
                              We bought the MiSeq when the PGM came out and was still comparable with the MiSeq. I don't know about Ion, but it seems the MiSeq simply works... consistently and as advertised. I've read in other reviews the Ion prep is very tricky but I'm not sure if that still applies with their new kits and machines. I would also take into consideration that there is a chance Ion won't survive given that they have fallen behind in all their promises. There are few niche applications where the PGM is better than the MiSeq, I'm not sure if these are enough to sustain their market, make sure that you don't buy a machine that will be discontinued in a few years.
                              Thanks for the info!

                              Comment


                              • Originally posted by vehuardo View Post
                                Hi all!


                                My institute will purchase a benchtop sequencer for bacterial genome sequencing. It will be used both for routine genome seq and (importantly) for infetious disease outbreak analyses. Hence, although only one of many important parameters, time from DNA isolation to results is important.

                                I am positively inclined towards the MiSeq, as I have only good experience with Illumina data (HiSeq and MiSeq). However, at a presentation at the institute, they weren´t really that impressive. Ion Torrent, on the other hand sent an expert on bacterial genome sequencing, who, it seems managed to sway a lot of people.

                                I find it difficult to make a sound comparison. The published literature largely favors MiSeq for quality of sequences and throughput. However, Ion Torrent claims that the Ion 318 v2 Chip yields improved quality. And throughput isn´t necessarily that important. They also claim that library prepping is fast (<2 hrs) and automated.

                                Also, what convinced people at my institute was data handling: the Ion Torrent seems to come with built-in software that can output variant calls and that can be tailor maid for various outputs (e.g. resistance gene mutations etc). This sounds nice, but I have a feeling that this way of doing things is not very flexible…

                                Some specific questions:

                                -Has anyone experience with long read MiSeq (2x250 or so) AND Ion torrent (418 bp reads)? Any thoughts on whats best?

                                -Is mate-pair sequencing on Ion Torrent something that must be done in a separate run following «normal» single end sequencing?

                                -Even though Ion Torrent is a lot more bulky and has more steps, It seems like it is a lot faster than MiSeq long reads. Is that correct?

                                -Is it problematic doing comparative genomic analyses with data from Illumina and Ion torrent together?

                                -M. tuberculosis (65% GC content) is among the bacteria that will be sequenced routinely. Ion Torrent seems to suck at high GC but I have only found one paper on this. How much is this of a problem? Ion Torrent showcased the use of Ion Torrent for quick resistance determination in M. tuberculosis, but this scheme relied on amplicon sequencing, which in my view is a bit like walking backwards into the future……

                                Please excuse this chaotic post, but there are so many questions...

                                All feedback appreciated,

                                Vegard
                                Hi Vegard,

                                I've been using both platforms for a while now and I'd say they are good at different things. Compared to the MiSeq, the PGM has lower max throughput, period. However the throughput of the PGM can be scaled depending on the chip you use. Currently there are three different chip sizes (314, 316 and 318). The 314 chip is the cheapest but also gives you the least amount of reads. We found this very useful as we would receive a small number of very high priority clinical samples that would not, by themselves fill a MiSeq run, thus wasting reagent.

                                When it comes to sample-prep, there's the IonChef that automates a lot of the pre-sequencing workflow, we've had it for a while now and it works really well. The only downside is that it requires 2 chips per run, so either you'll have to run 2 chips concurrently (not necessarily with the same libraries mind you) or have 2 PGM's. The library prep using the Chef is also straighforward, minimizing user error. There is also a new chemistry called Hi-Q that decreases error rates and increases overall sequence quality.

                                The IonTorrent server that takes care of the data can indeed be made to do variant calls and similar, generally we preferred to download the data instead and use CLC for mapping and variant-calling so i don't have that much experience with the inbuilt one. The server does support plugins though, so you can easily write your own pipeline in perl/python and make it run on your data directly on the server.

                                -I'm using both, mainly you see a difference in error profiles, the PGM is more inclined at having troubles in homopolymers while the MiSeq is more evenly spaced out.

                                -Mate pair on the PGM is fairly new, but it does not require an extra step, the sample prep is more complicated though.

                                -Running time varies a bit with what kind of chip you use, but usually its something like 6-10 hours after loading it on the instrument. The chef requires an additional 10-12 hours if i remember correctly, so we usually loaded the chips into the chef before we went home and then ran the PGM the morning after.

                                -When combining datasets, the different error profiles could mess with your analysis, there are a few read-error correction tools available (Hammer from the SPAdes pipeline for e.g.) that could help.

                                -We routinely used the PGM for bacterial sequencing (Listeria and other food-borne diseases) but also for parasites and similar. The PGM performed admirably at both tasks, from 30% GC to 65% as far as we could tell.

                                Bottom line:
                                If you have a large volume of samples that arrive continuously (so you can maximize the throughput of the MiSeq) and turnaround time is not a critical aspect, the MiSeq is probably the better choice. If you have a varying amount of samples that need to be turned around quickly, you are better of with a PGM.

                                //tracer

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