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  • SOAPdeNovo, get the contigs

    Hello all,
    I am writing this message because I will need help with SOAPDeNovo. Indeed, I made an assembly of Novo with this tool and I want to recover the final contigs. I'm outputting two files. The first file in .contig corresponding to contig sequences without using mate pair information . The second file is in .ScafSeq containing scaffold sequences.
    On the SOAP website , it is specified that the final contigs can be extracted by decomposing the scaffold sequences at the level of the gap regions.
    I would like to know how to achieve this decomposition in order to get the contigs?
    Hoping that you could help me I wish you a great day.
    Cordially
    (Sorry for my bad level in english)

  • #2
    Why not use the scaffolds ? These are the final contigs organised into scaffolds by using the supplied probably mate pair info. This is what I have always used.

    If you still want the contigs, maybe just break the scaffolds at long N stretches ?

    If its an illumina assembly, it is likely to be pretty awful. Long reads are the way to go these days as I'm sure you know.

    Comment


    • #3
      Hello, I want to thank you for your answer.
      I wanted to recover contigs because I want to scaffolding from two files containing separate contigs.
      Thank you very much for your response and your help

      Comment

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