[mira_talk] Re: clusterise big input

On Montag 04 Mai 2009 Laurent MANCHON wrote:
> I need to make contigs using mira2 but my input file contains 450 000 ESTs.
> So, i need to use different percent of alignment like 100%, 90%, 80% and
> generate contigs and ACE files.
> Do you know if Mira is able to treat this big input and which options i
> need to use to perform this task ?

The input size is no problem. However, MIRA is an assembler and not a 
clusterer. What you should do is: assemble with MIRA and take that output 
(contigs + singlets + debris) to a clusterer.

You *could* go by hand (or a wrapper), using multiple calls of MIRA in a 
fashion like this: assemble all at 100% (setting all the appropriate flags, 
there are a few I'm sorry). Then, taking out the contigs formed and using just 
remaining singlets and debris, assemble all at 90% in the next stage, etc.pp 

Regards,
  Bastien

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