[mira_talk] Re: Environmental samples
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 12 Aug 2009 23:32:25 +0200
On Dienstag 11 August 2009 Sven Klages wrote:
> Hi All,
> I am looking for an "optimal" parameter set to assemble environmental
> (metagenome) 454 titanium shotgun data (or hybrid with sanger).
>
> Any DOs and DONTs regarding parameters?
Hi Sven,
the closest thing to assembly of environmental samples I ever did was assembly
of EST from several different strains, but there I knew which read came from
which strain.
> A while ago I assembled a dataset like this:
>
> -job=denovo,genome,normal,sanger,454 -highlyrepetitive \
> -LR:mxti=yes -SK:not=30:mnr=yes -GE:kcim=yes \
> -AS:sd=yes:mrl=50 -CL:pvlc=yes:bsqc=yes \
> 454_SETTINGS -ED:ace=yes
> Results were OK ...
Except -AS:sd and -GE:kcim are eating away lots of memory for probably little
benefit in such a project, no further comment from my side. There MAY be other
things one has to take care of, but then there not immediately obvious to me.
B.
--
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:
