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  • Basic questions of MiSeq as a platform

    I've been looking for what I thought was the simplest questions, but have problem finding it.
    My lab is thinking about perhaps getting an Ion Torrent or a MiSeq.
    Ion Torrent has 3 different chips 314/316/318, each with increasing sequencing capacities.
    What are the equivalent of MiSeq chips? What are the running capacities (i.e., total amount of sequencing per lane and per chip) for MiSeq chips?

    Thanks in advance.

  • #2
    With MiSeq you will always buy the same number of potential reads (about 15 million). You may only decide what read length you want to choose: 1x50bp, 2x150bp or 2x250bp.

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    • #3
      Hi!

      I have the same problematics finding it. I read everywhere that reads are between 12 and 17 million, but at the same time in Illumina website I see there are 3 kinds of flow cells (Standard, Micro and Nano) up to 17M, 4M and 1M. Does anybody know something about it?

      Thanks!

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      • #4
        Originally posted by edgard View Post
        Hi!

        I have the same problematics finding it. I read everywhere that reads are between 12 and 17 million, but at the same time in Illumina website I see there are 3 kinds of flow cells (Standard, Micro and Nano) up to 17M, 4M and 1M. Does anybody know something about it?

        Thanks!
        I've looked all over the MiSeq page on Illumina's website, but I can't find the "standard, micro and nano" flow cells that you reference. Can you point to a specific link?

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        • #5
          This page from Illumina spells out what the MiSeq output options are (based on single read vs paired end and read length):

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          • #6
            The nano and micro kits were just made available and should be order-able soon. Not sure when they will be shipping yet.

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            • #7
              Originally posted by hoisinjl View Post
              The nano and micro kits were just made available and should be order-able soon. Not sure when they will be shipping yet.
              Oh, yeah, here they are:
              Documentation, product files, FAQs, and other support resources for the MiSeq System


              I haven't heard Illumina talk about these. Do you know what they've been saying? My guess is they're making smaller chips to keep the run times really short to help compete with the PGM.

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              • #8
                Looks like faster time by imaging less. Info from my FAS - estimates at the moment:

                1. Micro (300 cycles): 4M reads. images 8 tiles. ~17hr runtime.
                2. Nano (300 cycles): 1M reads. images 2 tiles. ~15 hour runtime
                3. Nano (500 cycles): 1M reads. images 2 tiles. ~24 hour runtime

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                • #9
                  Originally posted by hoisinjl View Post
                  Looks like faster time by imaging less. Info from my FAS - estimates at the moment:

                  1. Micro (300 cycles): 4M reads. images 8 tiles. ~17hr runtime.
                  2. Nano (300 cycles): 1M reads. images 2 tiles. ~15 hour runtime
                  3. Nano (500 cycles): 1M reads. images 2 tiles. ~24 hour runtime
                  Hmm, that's faster, but not THAT much faster. The 500 cycle standard flow cell supposedly takes 39 hours. So with the nano you're getting 1/15th the output but with <50% time savings. That doesn't seem that compelling to me. Maybe the reagents are a lot cheaper?

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                  • #10
                    I hear the flow cells are the same...just portions of the glass are etched/marked over so you can't use a "nano" flow cell for a full size run (by sneakily disabling the RFID on the nano-cell and using an override code for a full size run). Doesn't seem that compelling if the individual cycle times aren't much faster (they probably need smaller channels/volumes to drive that variable).

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                    • #11
                      Presumably they are betting that there are markets which highly value shaving off even 12 hours -- perhaps some amplicon sequencing diagnostic applications?

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                      • #12
                        I guess they want to offer the same "flexibility" as on the PGM regarding different output volumes depending on needs. It will be interesting how much they charge for those truncated kits given that the reagent production costs will presumably be the same as for the full kits. I guess margin is high enough so that they can discount those considerably nonetheless.

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                        • #13
                          I see. I was wondering why I couldn't find "smaller" chips for smaller runs. They actually don't exist.
                          By the way, when I look at the cost comparison such as this:


                          Does it include the Chip plus the library reagents? Or just the chips, or just the reagents?

                          Thanks.

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                          • #14
                            For us, the Nano kits are about 45% cheaper than the standard kits. The Micro kits are about 15% cheaper.

                            I guess it could be useful for people who have single samples to sequence at a time, where total cost is more important that per-base or per-sample cost (with multiplexed runs).

                            Cheers,

                            Scott.

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