Greetings. I have some denovo assembled contigs (Velvet 1.2.10) made from 250bp MiSeq (Illumina) reads. After I make the contigs, I normally extend and scaffold them using SSPACE v1.0. This usually goes off without a hitch with my old 100bp GAiix data, however it's not working with SSPACE apparently because it's not detecting that the reads are actually paired (" Unsatisfied pairing logic within contigs"):
Any ideas on how to fix this or just use a better extending and scaffolding program?
Code:
READ PAIRS STATS: Assembled pairs: 225450 (450900 sequences) Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 513 +/-20.52): 0 Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 0 Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 225450 --- Satisfied in distance/logic within a given contig pair (pre-scaffold): 0 Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 0 --- Total satisfied: 0 unsatisfied: 225450
Any ideas on how to fix this or just use a better extending and scaffolding program?
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