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  • De Novo Assembly - Illumina GAII & HiSeq 2000 Data

    Hello,

    I have successfully assembled Illumina GA II and Illumina HiSeq 2000 data using ABySS for various K-mers. However, I would like to know if there is a way to combine both Illumina GAII & Illumina HiSeq data and re-assemble it. Should I combine the Illumina data or their respective Kmer? Can ABySS re-assemble an already assembled data? I would really appreciate your help.


    Thank you,

    -Milo

  • #2
    Originally posted by milo0615 View Post
    Hello,

    I have successfully assembled Illumina GA II and Illumina HiSeq 2000 data using ABySS for various K-mers. However, I would like to know if there is a way to combine both Illumina GAII & Illumina HiSeq data and re-assemble it. Should I combine the Illumina data or their respective Kmer? Can ABySS re-assemble an already assembled data? I would really appreciate your help.


    Thank you,

    -Milo
    It is possible to combine 2 different dataset and do an assembly.

    However, don't re-assemble an already assembled data, that will mess up the data a lot. So in this sense, your choice can be combine the illumina raw data, do QC, and try the assembly again . For post-assembly process, in my opinion it might be okay to do a clustering by cdhit or tgicl (not really popular).

    Comment


    • #3
      Originally posted by RyNkA View Post
      It is possible to combine 2 different dataset and do an assembly.

      However, don't re-assemble an already assembled data, that will mess up the data a lot. So in this sense, your choice can be combine the illumina raw data, do QC, and try the assembly again . For post-assembly process, in my opinion it might be okay to do a clustering by cdhit or tgicl (not really popular).
      Hi RyNkA,

      I am going to use ABySS to do a paired-end assembly of the multiple libraries. Thank you for your reply.

      Comment

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