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  • Recommendation for illumina library prep automation

    I wonder if anyone has experience or good knowledge of following NGS library prep (RNA-Seq, DNA and Agilent sequence capture) automation systems (pre-PCR) re their pros and cons to share. I am looking for a walkaway (as much as possible) high throughput (12-96 prep) system.

    1- Hamilton NGS STAR
    2- Beckman Coulter Biomeck FXp
    3- Agilent NGS Bravo Option B

  • #2
    Not considering a Zephyr from PerkinElmer?

    We have FXp, Sciclones and STAR platforms, although only the former two are doing NGS library prep. We have a suite of PE platforms (Sciclones, NGS Express and Zephyr). To be honest if you're not doing anything unusual the Zephyr will be a good bet. FXp looks a bit like overkill as does the NGS STAR for your kind of throughput - and will take up a lot more lab real-estate than a Zephyr.

    Just check all your applications are supported/validated on whatever platform you buy. The Bravo always looks a bit limiting to me compared to a more generalised platform. I've had access to one in the past for SureSelect, but I do wonder how responsive Agilent would be if you want to do other capture applications on there..
    Last edited by Bukowski; 05-04-2016, 05:23 AM.

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    • #3
      Thanks Bukowski. Zephyr seems to be good for post PCR applications. I am looking to high end systems to have high throughput capability for future needs. Lab space is not an issue. Sciclone G3 NGSx also looks like a good candidate. I wonder if you would have any comment on your Sciclones and STAR platforms shortcomings or advantages.

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      • #4
        The Sciclones are great, to the point we have 3 of them. My automation experts would probably say they're a little easier to work with than the STAR platforms. We get great support from PE (we do from Hamilton too to be fair). As I said our STARs don't do NGS work - they're colony picking, miniprepping, plate reformatting systems for a different lab.

        I'd debate that any of them were really 'walk away' platforms. I agree at first glance the Zephyr is marketed mainly as a post-PCR platform. We have pre/post Fxp, the Sciclones are all post-PCR, our Zephyr is pre-pcr.

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        • #5
          Hi Bukowski,

          are you doing any NGS library preps with the Sciclones? If so which kits/protocols are you using?
          Our Sciclone NGS is definitely not a walk-away solution and the scripts provided for example by PE and Kapa have considerable bugs. The Nugen scripts are simpler but more reliable.

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          • #6
            Hi Bukowski,

            What Pre-PCR preps are you doing on the Zephyr? We mainly use ours for bead cleanups and that's it.
            We use the NGS Express for some pre-PCR stuff. It's a bit limited if you want to do large sample numbers, but for small batches it may work. Still have issues with any TruSeq preps, but Nextera XT and Nextera work ok.

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            • #7
              Originally posted by luc View Post
              are you doing any NGS library preps with the Sciclones? If so which kits/protocols are you using?
              Our Sciclone NGS is definitely not a walk-away solution and the scripts provided for example by PE and Kapa have considerable bugs. The Nugen scripts are simpler but more reliable.
              I originally had a sentence in my first reply that I edited out - the Sciclones, as you point out, are not really walk-away solutions, but I think this is a bit of an automation myth anyway.

              We use the Sciclones for RNA and DNA library prep and exome capture mostly. The latter is mostly Nimblegen/Mycroarray. I don't think we run any unmodified 'off the shelf' protocols, but I have a number of staff who are quite proficient with developing scripts so we're not too worried about development/debugging. We find Bioo invest time in the Sciclone platform with their kits.

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              • #8
                Our lab currently runs Agilent SureSelect capture (slightly modified protocols) on the Bravo Option A (we have 3). To be honest we're not that impressed with it. If we had gotten the option B, it might have improved the ability to "walk away", but I still find the deck extremely limiting. The pipetting head can only access certain parts of the deck in certain ways, so there can be quite a bit of planning that goes into how you need to set-up your deck.

                We have had multiple problems with the motors, which is causing our tips to not apply correctly, which then causes pipetting errors. We have had to constantly adjust teachpoints to ensure it's lining up properly with the plates/tips.

                The customer service is also pretty lacking because it seems there is only one person who actually services and programs the Bravo in the whole US. This has caused us many delays with getting questions answered, machines fixed, and protocols made. The software and programming protocols are not intuitive, so it usually requires contacting that one rep unless it's an incredibly simple change.

                Overall, if you're planning on using Agilent's protocols out of the box, without much customization, it could be a great, simple, robust instrument. You definitely have to be one step ahead of the Bravo. It cannot tell if anything is incorrect on the deck, and will crash into something if something is off. It definitely doesn't have any fancy features, but I do find it's great at performing bead separations and is great with accuracy when everything is calibrated correctly.

                Hope this helps! Although we will continue with these for the time being, we are looking into other instruments that we can automate the SureSelect capture protocol on. I'm also extremely interested in anything anyone say about some of the other liquid handling instruments.

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                • #9
                  Beckman NGS

                  Just wanted to drop a link to our NGS Sample Prep Automation page if you want to give us a look!

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