[mira_talk] Re: Problem with Paired 454, MP Illumina, MIRA and Bambus

  • From: Bastien Chevreux <bach@xxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Fri, 22 Jul 2011 00:25:25 +0200

On Thursday 21 July 2011 18:21:47 Evan wrote:
> Once I have contigs that have been scaffolded with one of the tools
> mentioned (Thanks everyone for brining these to my attention), what are the
> best Mira parameters to help fill in some of the gaps of NNNNN's?

Welcome to the longest and most expensive part of every genome sequencing and 
assembly project: finishing.

That's less a question of MIRA then ... more of your eyeball, grey matter and 
a good finishing program. You'll have to ask: what is in the N stretch? A 
repetitive sequence or something which was not sequenced or which MIRA threw 
away (for whatever reason)? Then make a guesstimate and perhaps perform a 
couple of primer walking steps to see whether you were right.

What you could try first though: perform a mapping assembly. Simply map all 
reads against the scaffolds you got (and perhaps assemble de novo reads that 
fell out) and see what this tells you at the places where you find Ns in the 


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