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Computer Suggestions for Minion Mk1c

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  • Computer Suggestions for Minion Mk1c

    Hi,

    We are looking to buy a computer since our IT department figured it'll be easier this way. I was wondering what type of computer system has worked best for you? We are currently in the looks of doing single cell genomics and cDNA analysis. It would be nice to know the general scope of how everyone is using nanopore (for what purpose) and which type of computer has worked best for it. Thank you in advance!

  • #2
    I assume you mean Mk1b; the Mk1c is a single enclosed unit, including sequencer, screen, and computer.

    There are two must-haves for a MinION sequencing computer: an NVIDIA GPU graphics card, and SSD storage.

    The GPU caller is hundreds to thousands of times quicker than the CPU caller, which is essential if you want to do more than one sequencing run every couple of weeks. See Miles Benton's GPU benchmark pages for information on what GPU cards work well enough for doing adaptive sequencing (i.e. selection of reads while sequencing is happening). If all you need to do is basecall after a run is finished (as all the other sequencers on the market do), then pretty much any new NVIDIA GPU card will do.

    The SSD card is needed because of the throughput of the device. It's not happy if reads can't be written quickly to disk.

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    • #3
      Hi all,

      i have the following laptop, can anyone tell if it can be used with Minion, we want to try to sequence a bacterial genome (no barcoding). Does the basecalling is done in the cloud?

      Intel Core i7-8565U (8MB Cache), 16GB 2666MHz DDR4,
      256GB M.2 PCIe NVMe SSD, AMD Radeon 520 with 2G GDDR5

      ------------
      SMART - bioinfo.uni-plovdiv.bg

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      • #4
        Originally posted by vebaev View Post
        Hi all,

        i have the following laptop, can anyone tell if it can be used with Minion, we want to try to sequence a bacterial genome (no barcoding). Does the basecalling is done in the cloud?

        Intel Core i7-8565U (8MB Cache), 16GB 2666MHz DDR4,
        256GB M.2 PCIe NVMe SSD, AMD Radeon 520 with 2G GDDR5
        Hello vebaev,

        I haven't ran a MinIon run in quite a while because I'm more used to Illumina machines. But I know that MinION Mk1B and Flongle (on MinION Mk1B) have the option to do basecalling on the computer locally. I believe all others can do basecalling in the cloud. I think depending on how you are doing it, the data processing can take some time.

        If you are using the Mk1c like the original poster, then I think the document I added will help you figure out if your computer will work.


        Attached Files

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        • #5
          Thanks. Yes I will use MinION Mk1B, so i hope i can do the sequencing on the above laptop, and that later to do the basecalling on more powerful machine?
          ------------
          SMART - bioinfo.uni-plovdiv.bg

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          • #6
            Originally posted by vebaev View Post
            Thanks. Yes I will use MinION Mk1B, so i hope i can do the sequencing on the above laptop, and that later to do the basecalling on more powerful machine?
            If you're using the Mk1B, then this document will help better to show you the laptop requirements.
            Attached Files

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