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  • Scaffolding contigs using SOAP

    Hey folks,

    I've been trying to scaffold some assembled contigs using sspace 1.2, soapdenovo and Bambus2.

    Each one has been giving its own set of troubles and none has completed in a satisfactory manner.

    This post is concerning the soap de novo scaffolder, which seems to be easiest to use.

    It seems my stumbling block here is the mapping portion of the process - nothing seems to map (I wish i could use an existing mapping file!)

    What is wrong with my commands?

    /usr/local/devel/BCIS/external_software/SOAP/prepare -c /usr/local/projects/IOAIR/PGIN/assembly/PG3/PGIN3/contigs.fa -K 55 -g PG3Full

    /usr/local/devel/BCIS/external_software/SOAP/SOAPdenovo63mer map -s /usr/local/projects/IOAIR/PGIN/assembly/PG3/pginv3.config -g PG3Full

    /usr/local/devel/BCIS/external_software/SOAP/SOAPdenovo63mer scaff -g PG3Full

    Here is the content of my config file:

    #maximal read length
    max_rd_len=100
    [LIB]
    #average insert size
    avg_ins=265
    #if sequence needs to be reversed
    reverse_seq=0
    #use for scaffolding only
    asm_flags=3
    #in which order the reads are used while scaffolding
    rank=1
    #fastq files
    q1=/usr/local/projects/IOAIR/PGIN/005_MDA3_Illumina/s_1_1_sequence.txt
    q2=/usr/local/projects/IOAIR/PGIN/005_MDA3_Illumina/s_1_2_sequence.txt
    #single fasta file
    f=/usr/local/scratch/dbrami/pgin/pgin3_sff.singles.fasta

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