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:
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