[mira_talk] Re: identify large insertions in mapping assemblies
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 15 Sep 2011 22:48:57 +0200
On Sep 15, 2011, at 18:46 , John Nash wrote:
> Do you have leftover contigs (or readings) which do not fit anywhere?
He probably will not have that if he made a pure mapping, i.e., without
-SB:abnc=yes. Which is actually what I recommend doing under normal
circumstances.
But then what can be done is to take unmapped reads (debris file) and simply
start a de-novo assembly on those and one quickly has the missing pieces
reconstructed. Works only for insertions though as pure genome shuffling will
not lead to insertions.
B.
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