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  • Hello

    I'm Mark, the author of EULER-SR a short read assembler.
    Last edited by mchaisso; 06-17-2008, 12:31 PM.

  • #2
    Hey Mark, Glad to have you!

    -+Eric

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    • #3
      Thanks for introducing yourself - care to post a link and a description to your assembler?
      The more you know, the more you know you don't know. —Aristotle

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      • #4
        Hi Mark,

        I'm sitting in Dr. Pevzner's talk at CHI and he's talking about EULER-SR...he had to skip the algorithmic discussion in the interests of time...but we'd love to hear about it in it's own thread...

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        • #5
          Unfortulately I missed most of that talk. He mentioned "Euler-usr" as in "ultra short reads"... is this a different version from Euler-SR, or is it just a slightly different name for the same thing, or did I misunderstand?

          Cheers,

          Scott.

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          • #6
            prolly have to register to download code ... looks like "frontier" research

            rudy

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            • #7
              Yeah, I realised after I posted that, that the EULER-USR is different from the SR version, but is not available until publication (which is fair enough I guess).

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              • #8
                A short description of EULER-SR

                Originally posted by apfejes View Post
                Thanks for introducing yourself - care to post a link and a description to your assembler?
                I'm a student of Pavel Pevzner, at UCSD. The assembler, EULER-SR, performs de Bruijn based assembly of reads. The "SR" in the name is a bit of a misnomer, since it can handle any length read. Our first publication on EULER-SR came out in Genome Research early this year:
                An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms


                If you're coming from an academic or research institution, you can download it from:


                The publication above is mainly regarding 454 reads, which I spent a lot of time getting it to work well on. Since then I've optimized it for Illumina reads as well, which mainly involved modifications that reduced memory usage - an E. coli assembly with 80X coverage runs on my desktop.

                If you want to assemble Illumina reads, go ahead and download the software. The code that is pending publication is for the special case when you've run the sequencer dry of reagents, producing 50-60nt reads that have low quality ends.

                For the next few days I've taken downloads offline since I need to improve the interface to euler-sr so that it is a bit more easy to run.
                Last edited by mchaisso; 06-17-2008, 12:54 PM.

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                • #9
                  Originally posted by ECO View Post
                  Hi Mark,

                  I'm sitting in Dr. Pevzner's talk at CHI and he's talking about EULER-SR...he had to skip the algorithmic discussion in the interests of time...but we'd love to hear about it in it's own thread...

                  I'll present a poster about this at ISMB next month... let me know if you want to hear about it now.

                  -mark

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                  • #10
                    Originally posted by mchaisso View Post
                    If you want to assemble Illumina reads, go ahead and download the software. The code that is pending publication is for the special case when you've run the sequencer dry of reagents, producing 50-60nt reads that have low quality ends.

                    For the next few days I've taken downloads offline since I need to improve the interface to euler-sr so that it is a bit more easy to run.
                    I'm interested in that. Is that what was discussed at the San Diego CHI conference? Is that going to be different version, or included in the standard download?

                    Cheers,

                    Scott.

                    Comment


                    • #11
                      Hello I was wondering how do you create the rul names file and if you would care to make a better description of how to make it and what does each column mean and all of that

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                      • #12
                        helo

                        hi every one.
                        am a 3rd year undergrad student form INDIA in pursuing my engg in BIOINFORMATICS.

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