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Celera assembler and metagenomic data - no contigs?

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  • Celera assembler and metagenomic data - no contigs?

    Hi, I'm trying to assemble some 100bp paired-end illumina reads using CA-7.0.

    The run did not fail, but resulted in no contigs. 70% of my reads were, however, in degenerate contigs.

    Is this expected because of a) short read lengths b) replicate sequences c) variation in the natural population d) all of the above (plus other stuff not listed)?

    I did an assembly of a subset of this data that went together quite nicely.

    thanks,
    Bill

    specfile:
    Code:
    fakeUIDs      = 1  #default 0
    
    #  TRIMMING
    vectorTrimmer  =  ca  # default ca; others figaro, umd
    doOverlapBasedTrimming = 1 # default 1
    obtOverlapper   =  ovl
    mbtConcurrency = 4
    mbtThreads = 4
    
    #  MERYL configuration
    merylMemory   = 2000   # default 800MB
    merylThreads  = 4      # default 1
    
    # OVERLAPPER configuration
    ovlOverlapper    = ovl      # default is ovl
    merSize       = 14 # default is 22
    
    utgErrorRate=0.03
    utgErrorLimit=2.5  # Allow mismatches over and above the utgErrorRate. This helps with Illumina reads.
    ovlErrorRate=0.05 # Larger than utg to allow for correction.
    cnsErrorRate=0.06 # Larger than utg to avoid occasional consensus failures
    cgwErrorRate=0.06 # Larger than utg to allow contig merges across high-error ends
    
    gkpFixInsertSizes      = 1
    
    doDeDuplication        = 1
    doChimeraDetection     = normal
    
    frgCorrConcurrency=4
    ovlCorrConcurrency=4
    
    unitigger     = bog
    utgBubblePopping = 1
    utgGenomeSize=1500000  # <- !!! I accidentally left this in from a different run
    
    doResolveSurrogates=1
    doToggle = 1
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