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  • Transposable Element Annotation in fungi

    Hi there,

    is there anyone of you who has experience of annotating transposable elements in fungi? I was thinking of using the REPET package (Flutre et al. 2011). Anyone having any experience of this package? Are there any other good alternatives?

    Thank you in advance!
    Kajsa

  • #2
    I have tried Tedna which is simple to run and delivers results in a convenient format, fasta I think. I am not sure how complete the results are on a large plant genome though since I have not tested others yet.

    I haven't tried REPET yet.

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    • #3
      Tedna, didn't hear about that before. Thanks!

      Comment


      • #4
        Do you know if the best method to find TEs is directly from unassembled reads or from an already assembled genome?

        Thank you in advance!

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