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  • Comparing the quality of de novo assembly from two runs' data

    We are using Miseq to sequence microbial genomes (~5Mb). In the first run (1#), library containing 12 samples were sequenced, and 6 samples were sequenced in the other run (2#). Obviously, the data of the 2# run have higher coverage depth that those of the 1# run. Therefore, I expected that the quality of de novo assembly data of the 2# run should be better than those of the 1#run. After analyzing by CLC Bio, I found that it is not true. Each sample from these two runs are shown as follow:

    Sample of 1# run Sample of 2# run
    N50 192439 261691
    Max length 461804 450288
    Average length 38501 8334
    Count of contig 145 688

    I dont understand why there are more contigs of 2# run that 1# run? Is that because of the high coverage? And how about the de novo assembly of these two runs?

    Thank you very much!

  • #2
    Is there anyone can help me????

    Comment


    • #3
      Some of your question is specific to CLC bio, which I don't use.

      What theoretical coverage did you actually achieve in the experiments? Are you using paired ends? What read lengths? What does the quality profile & insert size distribution look like for each? Are your samples very closely related, or perhaps not?

      If the libraries are quite different & poorer libraries are concentrated in the second run, then that might explain things.

      Comment


      • #4
        Krobison, thanks for your reply. The coverage of the 2# run is around 140x. I used paired ends 2x250. The insertion size of the 2# run looks longer than that of the 1# run from Bioanalyzer data. The samples are very closely related.


        Originally posted by krobison View Post
        Some of your question is specific to CLC bio, which I don't use.

        What theoretical coverage did you actually achieve in the experiments? Are you using paired ends? What read lengths? What does the quality profile & insert size distribution look like for each? Are your samples very closely related, or perhaps not?

        If the libraries are quite different & poorer libraries are concentrated in the second run, then that might explain things.

        Comment

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