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  • velvet

    hi After running velvet assembly I got Estimated Coverage = 25.12000
    Estimated Coverage cutoff = 10.250000
    Final graph has 11106 nodes and n50 of 498, max 13308, total 243547, using 221137/2500000 reads, so I have 3 questions here.

    1) what does this max 13308 ( It is the maximum contig length obtained)
    2)what does this total 243547 refers to?
    3) should I run the velvet again by using the obtained estimated cov cutoff and estimated coverege (for eg here should I run velvet again using cov_cutoff 10
    est_coverege 25)

    can any one answer this???

    thanks

  • #2
    1) Yes, it's the length of the longest contig you got.
    2) It's the sum of the length of all your contigs.
    3) You should probably try out the velvetOptimizer.pl script that is distributed along Velvet. Or you can join the Velvet mailing list and ask there.
    L. Collado Torres, Ph.D. student in Biostatistics.

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    • #3
      using 221137/2500000 reads
      that is a very low read usage - i would focus on figuring out why so few of your reads are making it into the assembly. Maybe they need to be trimmed further?
      --
      Jeremy Leipzig
      Bioinformatics Programmer
      --
      My blog
      Twitter

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      • #4
        hi zingster thnx for ur reply ...but my read length is 75 bp, do u think it should be trimmed further.

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        • #5
          Trim on quality, not length
          Joseph Fass's script does soft trimming - try 10, 15, and 20

          --
          Jeremy Leipzig
          Bioinformatics Programmer
          --
          My blog
          Twitter

          Comment

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