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  • mandar.bobade60
    Member
    • Jun 2013
    • 14
    #1

    Finding contaminant contigs in assembly

    Hi,

    I have generated plant mitochondrial assembly for which I would like to find contamination from chloroplast as well as nuclear genome. I have also run BlastN using same species nuclear genome and chloroplast genome database, and now with results I have some alignments with multiple scaffolds generated.

    My question is, if it is wise cutting down sequences from assembly which are having high identity with substantive e-value with subject sequences or I need to see some other criteria along with identity and e-value?

    Any help would be highly appreciated...
    Tags: None
    • bastianwur
      Member
      • Feb 2014
      • 98
      #2
      What about the length?
      Longer alignment > smaller one.

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