[mira_talk] Re: assembly parameters and more

Hi Davide,

Davide Sassera (davide.sassera) wrote:
> mira -project=050309 -job=denovo,accurate,454,sanger,genome -GE:not=2
> -SK:pr=97:mnr=YES -AS::rbl=8:nop=10:urdsip:8:klrs=1 454_SETTINGS -AS:mrl=30

I would think that parameter -AS:mrl=30 is not really useful. You have
high coverage and short reads will not help with contig joins. And for
titanium and signal processing 2.0.00.22 from roche we see quite a
number of short reads. Better get rid of them.

Also parameters:
-AS::rbl=8:nop=10:urdsip:8:klrs=1
should be written
-AS:rbl=8:nop=10:urdsip=8:klrs=1
but this is probably only email mistyping, right?

I do some projects with similar size (without sanger) and on similar
hardware and mira finishes it in 8 - 10 hours, not eating more than 10G
RAM with -SK:mnr=no (default). With -SK:mnr=yes it takes longer, but not
with more memory. And I never used -SK:pr=97 and -AS:mrl=30 parameters.

Hope my experience helps a little.

Greetings,

Jan Paces

Institute of Molecular Genetics
Academy of Sciences
Czech Republic

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