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  • How can be possible? (Velvet)

    I provide 5 reads to velvet (one read with 600 bp in size and the other four with 70 bp). After running , velvet returns an assembly with one contig with 572 bp in size. How can be possible an assembler returns a contig smaller than one of the reads???

    Best regards,
    André

  • #2
    Originally posted by aloliveira View Post
    I provide 5 reads to velvet (one read with 600 bp in size and the other four with 70 bp). After running , velvet returns an assembly with one contig with 572 bp in size. How can be possible an assembler returns a contig smaller than one of the reads???
    What was the command line you used to run Velvet?

    (It's an artifact of your low coverage, and edge-effects of k-mers)

    Comment


    • #3
      May I ask a noobish question? Is it 5 reads as in "Five pieces of DNA sequence being read by some method" and if yes, how did you end up assembling it? No insult meant, I'm really curious.

      Comment


      • #4
        Originally posted by A_Morozov View Post
        May I ask a noobish question? Is it 5 reads as in "Five pieces of DNA sequence being read by some method" and if yes, how did you end up assembling it? No insult meant, I'm really curious.
        I think the user is just testing Velvet, and is wondering why, if they feed it 5 sequences, one of which is 600bp, why do they get a final contig out that is shorter than 600bp. ie. what happened to the other 28bp.

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        • #5
          Have you looked at the final contig and see which part is missing? Does any of your other four sequences contain a nearly similar sequence (e.g. one bp difference) than the missing part. Velvet uses k-mers (provided by the option 'hash_length' with velveth), if you have a k-mer that is near identical, the assembler does not know which path to choose. Example;

          GATAGAGTAGAGA
          GATAGAGTAGAGT

          The assembler does not know if it should choose the A or T here. Look at the last x bases (where x depends on the set k-mer) of your contig, and see if any of the other four reads contains this k-mer.

          Regards,
          Boetsie

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