[mira_talk] Re: Mira assembly with reference
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 15 Apr 2011 23:45:55 +0200
On Friday 15 April 2011 10:45:07 Peter wrote:
> On Thu, Apr 14, 2011 at 9:41 PM, Andrei Tudor
> > I am wondering if it is possible to assemble some 454 reads, but using a
> > reference. I want to see if it will give better contigs.
> Yes, you can give MIRA a backbone sequence in de novo mode.
While it is possible, it is probably not what Andrei wants.
Loading a backbone in de-novo still performs a mapping assembly ... but with
de-novo parametrisation. Not sure this will work as expected.
Andrei: what you probably ask is whether MIRA can assemble some reads de-novo
using a given sequence as guide on how to build together and guide contigs.
Right?
If that was your question: no, this is not possible.
When given a backbone (reference sequence) MIRA will alway first perform a
mapping assembly using your 454 reads. If you ask nicely and use the right
incantations, MIRA will also assemble de-novo all reads it could not map. The
command line for that is (in principle):
mira --project=... --job=mapping,genome,454,accurate
-AS:nop=5 -SB:abnc=yes
...
and other options at will. Beware: instead of a mapping assembly (quite
quick), this has the time and memory foorptrint of de-novo (can be quite
long).
B.
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