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  • A new fruitfly genome de novo sequencing

    I have no experience in de novo genome sequencing, and i have a now project:

    A fruitfly genome de novo sequencing, and i want to use the Allpaths pipeline to assembly the genome, and want to use 180bp + 3K insert size illumina Hiseq 2000 sequencing, each libray squence one lane (>30Gb),

    Dose this work?

    Can anybody give me something advice?

    Thanks!

  • #2
    It's a good start, but only just fulfilling the minimum ALLPATHS_LG requirements. Adding more libraries of larger jump sizes might make for a better assembly. I just hope you have enough compute capacity/memory/disk space...

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    • #3
      Originally posted by nextomics View Post
      I have no experience in de novo genome sequencing, and i have a now project:

      A fruitfly genome de novo sequencing, and i want to use the Allpaths pipeline to assembly the genome, and want to use 180bp + 3K insert size illumina Hiseq 2000 sequencing, each libray squence one lane (>30Gb),

      Dose this work?

      Can anybody give me something advice?

      Thanks!
      By Hiseq 2000 sequencing and 30Gb data, should be 200x coverage for fruitfly, it's supposed enough for genome assembly. Also, you can use other pipeline to analysis data in the same time, like SOAPdenovo etc.
      Tom Tschannen, Ph.D

      eFLY Bioinformatics Technology
      www.eflybiotech.com
      Email: [email protected]

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      • #4
        Originally posted by nextomics View Post
        Can anybody give me something advice?
        You certainly have enough data in terms of paired end coverage, but that doesn't really ensure it can be assembled.

        I have no idea how complex a fruitfly genome is in terms of repeats and near-repeats (tandem or otherwise), but it would need to pretty simple to get away with just one size of mate-pair data.

        Then again, perhaps it is simple - maybe try an illumina read simulator using the drosophila genome, and see how well you can re-assemble it from simulated datasets.

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