Thread: Denovo assembly
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Old 05-06-2013, 06:38 AM   #2
krobison
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Location: Boston area

Join Date: Nov 2007
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If you have a reference available, then mapping your contigs back to it might give some insight into the nature of the breaks. Some may simply not be crossable using Ion Torrent technology -- large repeats in particular. Some may be missed overlaps; you may be able to identify errors that prevented joining, but since CLC is a black box there probably isn't much more debugging that can be done with that. You can play with the parameters, but I don't have any experience with CLC to suggest which to play with.
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