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  • How to identify different bacterial strains in the same sample

    I have Illumina sequencing of a bacterial sample collected from a patient. I suspect it's a mixture of multiple strains of the same bacteria, but I don't which strains are in there. Is there anyway to identify

    1. if this sequence sample is a mixture of different strains?

    2. how many and what strain are in there?

    Thanks.

  • #2
    How to do this in practice: http://seqanswers.com/forums/showthread.php?t=16812

    Analysis (see post #2) in this thread: http://seqanswers.com/forums/showthread.php?t=31565
    Last edited by GenoMax; 07-02-2013, 11:43 AM.

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    • #3
      Thanks. I'm not sure how this would help in my case. I'm not trying to do any phylogeny analysis. I just need to know if sequence I have was from one pure bacterial strain or from multiple strains.

      Originally posted by GenoMax View Post
      How to do this in practice: http://seqanswers.com/forums/showthread.php?t=16812

      Analysis (see post #2) in this thread: http://seqanswers.com/forums/showthread.php?t=31565

      Comment


      • #4
        Originally posted by shiningway View Post
        Thanks. I'm not sure how this would help in my case. I'm not trying to do any phylogeny analysis. I just need to know if sequence I have was from one pure bacterial strain or from multiple strains.
        My fault. The title on your original post made it sound (to me) like you were interested in identifying bacterial strains not specifically strains of the same species.

        If the strains are expected to have small differences then this would be a difficult problem.
        Last edited by GenoMax; 07-02-2013, 12:43 PM.

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