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SPAdes: does contig with node id has/refer coverage?

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  • SPAdes: does contig with node id has/refer coverage?

    Hi Members,
    I'm working on bacteria genome, illumina Hiseq paired end reads.
    Used:
    - trimmomatic with illumina adapter file.
    - spades for assembly with careful flag, bayes hammer correction.

    I get 2 fasta files: contigs and scaffolds.
    Contigs and scaffolds file give output in below fashion:

    scaffolds-
    >NODE_452_length_82_cov_291.815_ID_903
    contigs-
    >NODE_488_length_109_cov_1.07407_ID_975
    My question:
    Does cov_1.07407 and cov_291.815 refer to coverage of the contig/scaffold?

    Thank you.
    Bioinformaticscally calm

  • #2
    Yes, like in Velvet, this is the average k-mer coverage of a contig/scaffold. Use the last k-mer length if you need to convert to read coverage.

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    • #3
      Hi,
      Thanks for your reply.
      I do not quite understand what you meant. I have not really well read/understood on Velvet. (Have basic knowledge that it works on de bruijn graphs and so so..)

      Originally posted by akorobeynikov View Post
      Yes, like in Velvet, this is the average k-mer coverage of a contig/scaffold. Use the last k-mer length if you need to convert to read coverage.
      My assembly ran on 21, 33 and 55 k-mer (default SPAdes run).
      Bioinformaticscally calm

      Comment


      • #4
        Originally posted by bio_informatics View Post
        Hi,
        Thanks for your reply.
        I do not quite understand what you meant. I have not really well read/understood on Velvet. (Have basic knowledge that it works on de bruijn graphs and so so..)



        My assembly ran on 21, 33 and 55 k-mer (default SPAdes run).
        Check this http://seqanswers.com/forums/showthread.php?t=1529 for k-mer coverage. Use k=55 for SPAdes in this case.

        Comment


        • #5
          Thank you for directing to that page.

          Indeed the below URL far better explains what I was looking for:

          http://seqanswers.com/forums/showthread.php?t=6887

          Merci!
          Bioinformaticscally calm

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