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  • david2
    Member
    • May 2010
    • 19
    #1

    454 re-sequencing pipeline for bar coded samples

    Hi,

    (not sure it's considered cross-posting, but as the I.SEQanswers is still in beta, I am also asking here)

    I'm looking into putting together a pipeline to detect variants from bar coded samples run on a 454. Is there any consensus out there which open source tools would be useful? Or is Roche's software the current best practice?

    Thanks,

    David
    Tags: None
  • genehuntergirl
    Junior Member
    • May 2010
    • 4
    #2
    Check out VIP. I have just installed it - it looks like it will do everything GSMapper does.

    Comment

    • sklages
      Senior Member
      • May 2008
      • 628
      #3
      URL?

      cheers,
      Sven

      Comment

      • genehuntergirl
        Junior Member
        • May 2010
        • 4
        #4
        Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline - PubMed
        http://www.ncbi.nlm.nih.gov/pubmed/20487544
        We designed an open-source database oriented pipeline that enables advanced analysis of 454/Roche GS-FLX amplicon resequencing experiments using SQL-statements. This modular database approach allows easy coupling with other pipeline modules such as variant interpretation or a LIMS system. There is a …


        For the paper. You can find in there. I don't know the URL offhand as I'm not on my work comp.

        Comment

        • david2
          Member
          • May 2010
          • 19
          #5
          Thanks

          Thanks for the link, this looks like exactly what I need, I will try it out!

          Cheers,

          David

          Comment

          • joa_ds
            Member
            • Dec 2008
            • 52
            #6
            I'm glad to see people actually using the VIP pipeline.

            We have been using the pipeline internally for almost a year now. But eventually, some bug will appear here and there. Please report any bug any of you might encounter, so I can fix it for a future releases.

            Any questions concerning the pipeline are welcome as well.

            Comment

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