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  • CloVR manual upgrade or QIIME separately?

    I'm running a MiSeq V3 300PE with 96-182 multiplexing for 16S microbiome studies.

    I'm currently using CloVR for my 16S analysis (as well as PEAR for read merging and FASTX-toolkit for trim etc.)
    I've noticed that some of the tools and databases within CloVR are out of date (uchime, greengenes, chimera database). Is it possible to update them manually or is it suggested to move away from CloVR and use QIIME/mothur/uparse manually rather than a package?

    Thanks for your suggestions,

  • #2
    There's a similar GUI interface for QIIME now:
    http://qiita.ucsd.edu/

    Honestly, if you can run stuff on the command line, which it sounds like you can, I'd just do that.

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    • #3
      I liked CloVR as it is mostly plug and play which makes it easy for me to make an SOP for other users in my group.

      Thanks for the qiita link, I've checked it out before but was hesitant to use it as it is currently an alpha. Is it experimental right now or are the changes to be made mainly ease-of-use and feature addition?

      Have you tried a local install of qiita to run it as a server or virtual server, is this a recommended method if I have decent CPU/RAM hardware?

      Thanks for the help!

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      • #4
        I've not used it myself, so I can't speak to development. But don't see why running as a virtual server would be an issue on a decent machine.

        Relating to your first point, I'm in a similar situation where other people in my group are less familiar with the CLI/scripting. The approach I've taken is to run the processing and basic analyses for them, and have them use rsync to retrieve the results. For QIIME, this works out nicely as they can simply use the html files to navigate around, and I try to include documentation about where any additional figures are located. Just my 2c...

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