[mira_talk] Re: hybrid assembly question

Hi,Bastien:

I produced 130Mb scaffolds from Solexa reads with SOAPdenovo, the longest 
scaffold is about 1Mb.  I used unaltered contigs/scaffolds without shreding 
them.  The organism genome size is about 200Mb.  Thank you.

> From: bach@xxxxxxxxxxxx
> To: mira_talk@xxxxxxxxxxxxx
> Subject: [mira_talk] Re: hybrid assembly question
> Date: Wed, 8 Jul 2009 01:08:09 +0200
> 
> On Dienstag 07 Juli 2009 周琦 wrote:
> > Hi, glad to have mira and the discussion forum here.  I'm a new guy to
> > mira, so not sure I did it right:
> > [...]
> > mira -GE:not=8 -fasta -project=hybrid -job=denovo,genome,normal,sanger,454
> > -notraceinfo
> 
> Hello Qi,
> 
> one first thing: I think you should tell MIRA not to clip the "sanger" reads: 
> "--noclipping=sanger"
> 
> But could you give some more info on what you did? I'm not sure I understand 
> what you mean with "130Mb assembled scaffolds produced by Solexa". Did you 
> take 
> unaltered contigs? If yes, did you shred the longer ones (>20kb)? How big is 
> the organism you try to assemble?
> 
> Regards,
>   Bastien
> 
> 
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