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  • Some probably very stupid questions on ray meta

    Sorry, apparently the following points are obvious to everyone but i am alittle at loss.
    I want to test ray meta for metagenome assemblies and compare it to Meta-Velvet.

    Apparently Ray Meta differs from the original Ray (citation from the respective paper by Boisvert et al, 2012: "The algorithms implemented in the software Ray were heavily modified for metagenome de novo assembly and these changes were called Ray Meta.")

    The Ray Manual states that you should use "Ray vanilla" for single genome assemblies and "Ray Meta" for metagenomes. However then it never mentions "vanilla" or "meta" or even "metagenomes" anymore.

    What is the difference between "Ray vanilla" and "Ray meta"?
    Are they two different programs? (I could only find downloads for Ray).
    Are they two seperate modules that are included with Ray? (Then which parameters do I have to give to use Ray Meta and not Ray Vanilla?)

    It sounds like a very promising alternative to Meta-Velvet but the manual is just not clear enough for my dumb brain.

  • #2
    It's not a stupid question, I have been wondering the same thing.

    I think Ray Meta is just Ray with the taxonomy and biological abundance options activated.

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    • #3
      It's not a stupid quetions. I had the similar question and asked the author in the email: "Dear authors: I found Ray use same command for single genome assembly and metagenomics assembly. But how does ray know the data is metagenomics or single genome sample?"

      Their response:
      Ray 2 (2.0.0, 2.1.0, 2.2.0) is an improvement over the older Ray 1 in the sense that the algorithms are generalized to work on both genomes and metagenomes.
      In our paper http://genomebiology.com/2012/13/12/R122 , we explained how we did it. You can read more about that in the Materials and methods. Ray Meta is really just a workflow for metagenome assembly provided by the Ray 2.x.y series. Also, Ray Communities allows you to profile gene ontologies and taxons in your sample. This is also part of Ray 2.

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