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  • number of contigs in velvet

    hi all , what is the approximate total number of contigs we should get in a velvet assembly? I would like to know this because i did assemblies with various parameters but i always get more then million contigs..

  • #2
    Use VelvetOptimizer.pl

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    • #3
      In a genomic assembly you should get exactly the number of chromosomes for that species or you've made a horrible mistake.

      Seriously, i think you are beginning to shoot from the hip with your questions to this board. Post some more specifics or do some research on your own.
      --
      Jeremy Leipzig
      Bioinformatics Programmer
      --
      My blog
      Twitter

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      • #4
        What are you trying to assemble?

        Here are some numbers from CLCbio tool: http://www.clcbio.com/index.php?id=1413

        Lesser, longer contigs are better, provided they are not incorrect!
        --
        bioinfosm

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        • #5
          re

          hello zingster ..iam very new to this kind of research and iam not expertise like you in bioinfo ....so only i have these kind of questions araises..im sry if iam hard..

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          • #6
            This thread reminds me of something...thanks...(will post the idea in the Site Feedback forum shortly...)

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            • #7
              Searching in the dark

              Yes, it's better we know the exact chr number. But not all the organisms we know their chromosome. A good way is to align to a closely related organism and then to check the left contigs.

              Originally posted by Zigster View Post
              In a genomic assembly you should get exactly the number of chromosomes for that species or you've made a horrible mistake.

              Seriously, i think you are beginning to shoot from the hip with your questions to this board. Post some more specifics or do some research on your own.

              Comment

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