[mira_talk] Re: Assembly genome pine

On Monday 24 November 2008 13:13, Rocío Bautista wrote:
> Nevertheless, I'm working with sequences of pine, it is a highly
> repetitive DNA and I believe that they can produce mistakes of assembly.
> I use:
>
> "mira -fasta -project=40B10 -job=denovo,genome,draft,454
> -highlyrepetitive -LR:mxti=yes -FN:xtii=40B10_traceinfo_in.454.xml
> -AS:nop=10 -AS:rbl=5 -AS:mrl=3"

Ummm ... why are you setting a minimum read length of "3" for Sanger reads if 
you do only a 454 assembly? Did you forget the "454_SETTINGS" in front 
of -AS:mrl? And 3 is really really really a bit small.

> What other parameters can I change to improve the result?

Use "normal" or "accurate" instead of "draft". They both use a whole bunch of 
parameters that "draft" dwitches off to get, well, a first draft :-)

If you worked with 2.9.26 or lower version, you might want to try the latest 
build which has a few new tweaks.


If you have really nasty repeats, try "-SK:mnr=yes", but be aware that this 
might mask away quite a bunch of data (adjustable via "-SK:rt").

Regards,
  Bastien

--
You have received this mail because you are subscribed to the mira_talk mailing 
list. For information on how to subscribe or unsubscribe, please visit 
http://www.chevreux.org/mira_mailinglists.html

Other related posts: