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  • SOAP scaffolder deleting 1nt every 1023 bases

    I have an assembly from AllPaths that I wanted to use 100M 35k insert read pairs and SOAP denovo's scaffolder to improve the scaffolding. It did but it appears to have deleted 1 nucleotide every 1023 bases in some scaffolds. Here are the details:

    The Allpaths assembly had used the following reads:
    240M 101bp read pairs with in insert size of 170 (overlapped)
    228M 101bp read pairs with an insert size of 250
    228M 101bp read pairs with an insert size of 375
    237M 101bp read pairs with a 2-4k insert size
    100M 101bp read pairs with a 30K insert size

    The results of this build was a scaffolded N50 of 61.5k but the assembly only used 18k of the 35k insert read pairs so I wanted to use SOAPs scaffolder to see if it could improve the N50.

    I started with the assembly results from AllPaths (which had already used the 35k insert read pairs once).

    Here is the commandline I used:
    _______________________________________________________________
    [waalkes]$ prepare -c scaffolds.fasta -K 63 -g SOAP_v1
    [waalkes]$ SOAPdenovo63mer-v1.05 map -s SOAP_scaf.config -g SOAP_v1
    [waalkes]$ SOAPdenovo63mer-v1.05 scaff -g SOAP_v1

    With the following config file:
    #maximal read length
    max_rd_len=101
    [LIB]
    #average insert size (I used median number from Rupali)
    avg_ins=29760
    #if sequence needs to be reversed
    reverse_seq=0
    #in which part(s) the reads are used (scaffold only)
    asm_flags=2
    #in which order the reads are used while scaffolding
    rank=1
    # cutoff of pair number for a reliable connection (default 3)
    pair_num_cutoff=3
    #minimum aligned length to contigs for a reliable read location (default 32)
    map_len=32
    #fastq file for read 1
    q1=/net/shendure/vol6/waalkes/stacks_tutorial/35kReads/s_4_1.fq
    #fastq file for read 2 always follows fastq file for read 1
    q2=/net/shendure/vol6/waalkes/stacks_tutorial/35kReads/s_4_3.fq
    _________________________________________________________________


    The scaffolded N50 increased to 95k but in looking at one of the new scaffolds I found that the soap scaffolder seemed to have deleted a nucleotide every 1023 bases in some scaffolds. Have you any idea what might have caused this?

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