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  • 454 sequencing data coverage

    Dear All,

    I am currently working on 454 sequencing data. The average length of reads is ~200bp, and coverage is ~8-10X.

    Does anybody tell me how the data coverage is? Is it ok or not?
    Because when I do annotation, I found many many single nucleotide changes (mutation/insertion/deletion).

    Thank you.

  • #2
    de-novo or refguided?

    We usually work with ~30x coverage when dealing with both denovo and refguided assemblies (FLX), Though you might need a bit less for refguided. This is for bacterial genome size projects (1-8Mb) here.

    Sven

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    • #3
      We usually do 20x de novo assembly. This works for either FLX or Titanium.

      Sounds that you are still doing FLX.

      454 Titanium paired end data improved a lot compared to FLX paired end. Now I would think perferrably, 10x shot gun, and 10x paired end.

      Recently I did a de novo assembly on a , 454 machine can run 2 pads in same runs. 1 pad for shot gun, another pad for paired end data in same run. The fungi assembly worked well for us.
      Last edited by hlu; 02-05-2009, 02:23 PM.

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      • #4
        Originally posted by hlu View Post
        454 Titanium paired end data improved a lot over compared to FLX paired end.
        hlu,

        I don't think the Titanium paired end kits are available yet. Are you doing a home brew paired end with Titanium?

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        • #5
          Originally posted by kmcarr View Post
          hlu,

          I don't think the Titanium paired end kits are available yet. Are you doing a home brew paired end with Titanium?
          I am using early access 454 Titanium pairs end kits.

          There are not out there yet public. I heard from 454 sales that they will be out possibly within a month. So it will be there soon.

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