Re: [wgs-assembler-users] overlap job

[Brian W. <th...@gm...>]

[resending to the list too, oops]

How many reads?  700k * 200 = 140 Mbp.

For starters, try

ovlHashBits         = 22
ovlHashBlockLength  = 200000000
ovlRefBlockSize     = 18000000
ovlThreads          = 4

This will generate jobs that need about 6gb memory each.  Increasing
ovlRefBlockSize will decrease the number of jobs but increase the run time
of each.  See
http://wgs-assembler.sourceforge.net/wiki/index.php/RunCA#OVL_Overlapper
for details.

3 or 4 days probably won't happen, 2-3 weeks is more reasonable, with a lot
dependent on the mate size and genome complexity (or lack thereof =
repeats).

On Mon, Dec 8, 2014 at 1:01 AM, Manjari Deshmukh <
man...@gm...> wrote:

> Hi
>
> i am running celera with 700000 reads each more  than 200 bp length and
> genome size is approx 1.3Gb. The celera has generated 438064 overlap job.
>
> I want to know if there is any method to increase the assembly speed. I
> want results in 3 or 4 days.
>
>
>
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