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  • Config file for soapdenovo2

    Hello everyone,

    I am new to assembly and I have a syntax question to ask:

    This is an example contig file as given on https://github.com/aquaskyline/SOAPdenovo2

    In the [LIB] section, we already specify parameters such as avg_ins, reverse_seq, asm_flags, rank etc then why do we again define the limits outside the [LIB] at the end of the file? Are those maximum values of these parameters?

    I tried to find this in the documentation but couldnt get any information

    Code:
    #maximal read length
    max_rd_len=100
    [LIB]
    #average insert size
    avg_ins=200
    #if sequence needs to be reversed
    reverse_seq=0
    #in which part(s) the reads are used
    asm_flags=3
    #use only first 100 bps of each read
    rd_len_cutoff=100
    #in which order the reads are used while scaffolding
    rank=1
    # cutoff of pair number for a reliable connection (at least 3 for short insert size)
    pair_num_cutoff=3
    #minimum aligned length to contigs for a reliable read location (at least 32 for short insert size)
    map_len=32
    #a pair of fastq file, read 1 file should always be followed by read 2 file
    q1=/path/**LIBNAMEA**/fastq1_read_1.fq
    q2=/path/**LIBNAMEA**/fastq1_read_2.fq
    [LIB]
    avg_ins=2000
    reverse_seq=1
    asm_flags=2
    rank=2
    # cutoff of pair number for a reliable connection (at least 5 for large insert size)
    pair_num_cutoff=5
    #minimum aligned length to contigs for a reliable read location (at least 35 for large insert size)
    map_len=35
    q1=/path/**LIBNAMEB**/fastq_read_1.fq
    q2=/path/**LIBNAMEB**/fastq_read_2.fq

  • #2
    It's not outside [LIB], it's a second library that is defined! So for every library you have, you start with a line "[LIB]", and then list all the parameters (specific for each library).
    In the example there is one paired end library and one mate-pair library.

    Linnéa

    Comment


    • #3
      Thanks a lot Linnéa!

      That explains it nicely and now I also understand the 'Library rank'.
      Thank you again

      Comment

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