Question: Minia estimated genome size
0
gravatar for stacy734
9 months ago by
stacy73420
stacy73420 wrote:

Hi everyone,

I'm experimenting with Minia for genome assembly of a eukaryote with a 500 MB genome size. I've had good luck adjusting the parameters to find the optimum, except for one: estimated_genome_size.

The manual suggests this: estimated_genome_size

And I have added this to the command line: -estimated_genome_size 500000000

With and without preceeding dashes, changing underscores to dashes, etc, but always get this result: ERROR: Unknown parameter '-estimated_genome_size' ERROR: Unknown parameter '540000000'

Further, the Minia options which are displayed as the result of the error do not include estimated_genome_size. Is this parameter no longer recognized, or does anyone have any suggestions?

Thanks for your help.

minia assembly genome • 363 views
ADD COMMENTlink modified 9 months ago by Rayan Chikhi1.2k • written 9 months ago by stacy73420
1

Which version of Minia are you using? The latest one (v2.0.7) doesn't need the estimated_genome_size, only input sequence-files are required.

ADD REPLYlink written 9 months ago by Rohit1.2k

Indeed, Minia versions >= 2 do not need this parameter anymore (http://minia.genouest.org/)

ADD REPLYlink modified 9 months ago • written 9 months ago by Rayan Chikhi1.2k
0
gravatar for Rayan Chikhi
9 months ago by
Rayan Chikhi1.2k
France, Lille, CNRS
Rayan Chikhi1.2k wrote:

Minia versions >= 2 do not need the genome size estimation anymore

ADD COMMENTlink written 9 months ago by Rayan Chikhi1.2k
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