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Ion Torrent vs MiSeq vs GS Junior

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  • #16
    "I've heard the runs times will be relatively the same for 200bp, and for 316/318."

    I thought the 318 was already out? Does anybody has some data on the 318? Does it really give you 200bp?

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    • #17
      As stated by Mr Robison, because of primers and specific key sequences your inserts can't be longer than 150bp.

      Ion 316 chip is just available to order in Europe. Ion 318 Chip should be available in September and the read lenght associated with this chip is 300bp.

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      • #18
        - PGM : 10Mb (314 chip), 100Mb (316 chip), 1Gb (318 chip)
        - MiSeq : 680Mb (2X100), 1Gb (2X150)
        - GS Junior : 1Gb, 500bp max by amplicon

        I have to correct your GS Junior statement:

        The instrument produces on average 100.000 reads and 35 Mb per run. But I heard if you really have an extremely good library you can push it to almost 50 Mb... I got with 80k reads 38 Mb out once...

        But I think that is the maximum of the GS Junior. The longer read lengths announced for 454 sequencing (700-1000) will only be available with a hardware upgrade to the big version.

        I think you have to be careful when setting "read length" == "total output". Especially for de novo the read length is very important as you will need more coverage with shorter reads (e.g. Sanger =>7X, 454 =>20X, Illumina =>30X). Increases in read length will shift the numbers left... I am also not sure if you can really solve all problems of de novo assemblies using mate pair/paired end sequencing of short reads...
        But for standard stuff like amplicons or short read mapping or experiments where you really need coverage you should go for PGM or MiSeq... probably PGM...

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        • #19
          Thank you Mucku for this relevant answer.

          I did not notice my mistake and you are absolutely right : total output of GS Junior is 40Mb (specification from Roche) and it will be 80Mb at the beginning of 2012.

          I agree with you, PGM looks good on the paper but we need more comparative scientific papers to have a better view of advantages/drawbacks of each machine.

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          • #20
            PGM ~50 Mb 314 chip and 170 Mb 316 chip @ Broad, data presented at ESHG. ~1.8 M reads with Q > 17 if I am not mistaken.

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            • #21
              I found these webinars of IonTorrent very informative.

              They also show data from the Broad Institute and others...

              http://kevin-gattaca.blogspot.com/20...-training.html

              As I remember the pH sensor doesn't really have a homopolymer problem... I think a hexamer is still called with a Phred 20 score. So I think part of the actual error might be not from the chemistry but from polymerase slippage during library preparation... Also the quality at position 100 is still extremely good, and you probably don't have to cut back so much of your reads because of low quality ends.
              The PGM has really potential, I hope that not all of it is marketing...

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              • #22
                Look at real data before you state it doesn't have a homopolymer problem. It really, truly does -- it isn't something that can't be overcome, but the instrument+software has to date had difficulty enumerating homopolymers, even ones shorter than 6.

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                • #23
                  Originally posted by krobison View Post
                  Look at real data before you state it doesn't have a homopolymer problem. It really, truly does -- it isn't something that can't be overcome, but the instrument+software has to date had difficulty enumerating homopolymers, even ones shorter than 6.
                  Sorry if it came across that I stated it doesn't have any problems... I have to apologize.
                  At this point there is so much competition in that area that probably only half of the information actually fits the systems and the other half are optimistic forward looking statements...
                  As I said I hope it is not all marketing...

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                  • #24
                    Real Comparison

                    I hardly tried to find some papers comparing that technologies but I have not been successful. Do someone knows some review, or paper showing the best characteristics of all these machines (IonTorrent PGM, Ilumina miSeq and Roche 4545Junior). As far as I see, here all the discussions are about what providers say in the catalogue?
                    Thank you very much

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                    • #25
                      Try this one:
                      "Field guide to next-generation DNAsequencers"
                      amazing review

                      Molecular Ecology Resources (2011) doi: 10.1111/j.1755-0998.2011.03024.x

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                      • #26
                        paper

                        I read the abstract but unfortunatelly from my university I have no access...I'll have to ask for it somewhere.
                        Thanks for the advice.

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                        • #27
                          Originally posted by amascarell View Post
                          I read the abstract but unfortunatelly from my university I have no access...I'll have to ask for it somewhere.
                          Thanks for the advice.
                          http://molbiol.ru/forums/index.php?a...post&id=112976

                          http://molbiol.ru/forums/index.php?a...post&id=112978

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                          • #28
                            Thank you very much genseq...you safed my life

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                            • #29
                              MiSeq vs. Ion Torrent vs. GS Jr. vs. FLX+ vs. PacBio...

                              Updated tables that compare all of the currently commercially available & announced upgrades for Next Gen platforms are available at:

                              http://www.molecularecologist.com/next-gen-fieldguide/

                              It has prices for the instruments & ancillary equipment, performance based on stated goals of upcoming releases, summary "grades" for each platform for specific uses, etc.

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                              • #30
                                Originally posted by BadDNA View Post
                                Updated tables that compare all of the currently commercially available & announced upgrades for Next Gen platforms are available at:

                                http://www.molecularecologist.com/next-gen-fieldguide/

                                It has prices for the instruments & ancillary equipment, performance based on stated goals of upcoming releases, summary "grades" for each platform for specific uses, etc.
                                I found the grades kind of subjective but otherwise very good information for comparing platforms.

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