[mira_talk] Re: How does MIRA use paired end information?

On Sep 15, 2011, at 23:54 , Evan wrote:
> So if MIRA has further passes to preform before it completes will it scan 
> through each contig and check for read pairs that are:
[...]
> And correct any inconsistencies by removing these reads from the contig and 
> placing them back into the pile of unassembled data?

Will you be very disappointed if I tell you hat for each pass, MIRA places back 
*all* reads into the pile of unassembled data? :-)

And yet it gets most repeats disentangled that way. Before I try to tell you 
it's simply magic: you might want to have a look at the thesis 
(http://chevreux.org/mira_papersnposters.html and there pages 32 and 81++), the 
article I have on miraEST in Genome Research 
(http://genome.cshlp.org/content/14/6/1147.full.pdf+html) as well as a couple 
of sections in the manual:

  
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_intro_miradiscernsrepeats
and
  
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_ref_snp_discovery
and
  
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_ref_tags_set_and_used

B.


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