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Old 04-01-2014, 09:03 AM   #1
Location: Maryland, USA

Join Date: May 2012
Posts: 60
Default Problem extending/scaffolding contigs with MiSeq 250bp reads?

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"):

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?
Genomics101 is offline   Reply With Quote
Old 04-02-2014, 06:04 AM   #2
Location: Oslo, Norway

Join Date: Nov 2008
Posts: 415

I am not familiar with SSPACE, but could it be that your version does not understand the new sequence IDs? See both versions at
flxlex is offline   Reply With Quote

denovo assembly, miseq 250bp, scaffolding, sspace

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