[mira_talk] Re: closing sequence assembly

On Montag 11 Mai 2009 Sucheta Tripathy wrote:
> I have a different type of problem here. Now I have a draft assembly and a
> bunch of BACs assembled  manually to the draft assembly. The result is in
> the form of --(contig1)---><--BAC--- ---(Contig2)---> format where there
> are certain amounts of mismatches and gaps in between. Although I know the
> orientation etc. I actually don't want to join them manually. Instead I
> would like to run an assembly of the said BAC and the 2-3 contigs that I
> know can be joined together. Can I use MIRA for this?

Sorry, no.

At least not directly. MIRA doesn't allow to use sequences larger than 20kb. 
What you could try (I've never done this but I see no reason why this should 
not work): fragment your contigs and BACs into, e.g., 20kb pieces with 15kb 
overlap and then try an assembly on that. If the overlap is strong enough 
between your BACs and the contig fragments, the join could be made.

However, I'd bring the contigs and BACs into the right order, import them into 
a finishing tool (gap4 inmy case) and use a "join contig" functionality there. 
Should be almost as quicj as the fragment approach and you have visual control 
whether the joins are ok or not.

Anyone having other suggestions?

Regards,
  Bastien


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