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  • Soap de novo trans parameters

    Hi all,

    I just recently trying to use SOAP denovo-trans for de novo assembly of a non-model species. I did try to run SOAP-trans but i'm kind of confuse about the options in the config file.
    ---------------
    3) asm_flags
    This indicator decides in which part(s) the reads are used. It takes value 1(only contig assembly), 2 (only scaffold assembly), 3(both contig and scaffold assembly).
    ---------------

    Which to choose in my case ? I have single end reads file, with read length ranging from 30-300

    Any suggestions

  • #2
    Without paired end reads you will only be able to construct contigs (not scaffolds). You can either specify 1 or 3.

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    • #3
      Originally posted by jebowers View Post
      Without paired end reads you will only be able to construct contigs (not scaffolds). You can either specify 1 or 3.
      Thanks for the answer.

      That's what i was doubt about, what if i specify 3 ? What will the program behave, will it just omit scaffoldings step ?

      Comment


      • #4
        Yes the scaffolding step will happen or not, but it will only look at zero paired ends so I expect it should not take long to run.

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