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  • SOAPdenovo2

    Hello everyone, I am new to this forum and new to using assembly tools as well. I am trying to use SOAPdenovo2 and tried to write the configuration file which is as follows :

    #maximal read length
    max_rd_len=36
    [LIB]
    #average insert size
    avg_ins=100
    #if sequence needs to be reversed
    reverse_seq=0
    #in which part(s) the reads are used
    asm_flags=3
    f=sample.fq

    I am using soapdenovo2 in steps. I tried to use the pregraph_sparse63mer version using this command :

    /pregraph_sparse63mer -s configfile -K 63 -z 1000000 -o output_graph -p 4


    The programs starts to build the graph but no nodes are allocated and it seems to parse the file but O kmer detected etc...

    I have tried with combinations of -k 23 and smaller values because my reads are very short (36 nt) in length and it is a bacterial file 88 MB

    I do not know if my parameters are correct in the config file but I am using only ONE FASTQ file.

    Thank you.

  • #2
    SOAPdenovo2

    If the file with your reads is in fastq format you should have
    q=sample.fq

    in the configuration file.

    Did you get any better results with -K 23 or smaller?
    Kmer size needs to be shorter than your reads.

    Comment


    • #3
      Hi, Thank you. Yes, it started to construct the graph and when I used the command soapdenovo2 63-mer contig -g output_graph , it produced a file named output_graph.contig

      However, the contigs are very small and in this format:

      >1 length 16 cvg_0.0_tip_0
      AAAAAAAAAAAAAAAA

      is that alright?

      I used the same pregraph_sparse command but used -K 15

      Comment


      • #4
        SOAPdenovo2

        Hi,

        A month ago, i was struggling with pregraph_sparse too.
        My problem was, as you stated "The programs starts to build the graph but no nodes are allocated and it seems to parse the file but O kmer detected etc..."

        I compiled from source in the first place. Then, i decided to give binaries a try, and it was finally working. Maybe this could solve your issue.

        Best,
        Erwan

        Comment


        • #5
          Hi thank you, I compiled from the source and the program is working but the length of the contigs are in the format that I stated above and does not seem right. Have you used Soapdenovo2 and are your contigs in the same format?

          Thank you.

          Comment

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