Question: running SOAP using 32G RAM
0
gravatar for reza
2.9 years ago by
reza210
Iran
reza210 wrote:

Our lab PC have 32G RAM and CPU 3.5GHz. i want to assemble my NGS paired reads using SOAPdenovo. My genome sequenced in two lanes. number of reads in each lane is 455 millions. Genome size in my project is 2Gb approximately.

my question, can i run SOAP via mentioned condition in our lab PC?

next-gen assembly • 775 views
ADD COMMENTlink modified 2.9 years ago by Rohit1.4k • written 2.9 years ago by reza210

Depends on the size of the genome you are trying to assemble. According to SOAP manual 150G may be required for a human genome. You can give it a try and see what happens.

ADD REPLYlink written 2.9 years ago by genomax69k

Probably not. You might try Minia, which is supposed to have a low memory requirement. But your best bet is to get access to a computer with much more memory; 256-512 GB.

ADD REPLYlink written 2.9 years ago by Brian Bushnell16k

You can have a look here about Minia, in particular Table 2 to have an idea of memory usage of Minia.

ADD REPLYlink written 2.9 years ago by edrezen720
0
gravatar for Rohit
2.9 years ago by
Rohit1.4k
California
Rohit1.4k wrote:

Soap-denovo definitely needs much more memory, in that case most other denovo assemblers do.

Minia does a great job at low memory. The assemblies are comparable to the big-memory assemblers, sometimes even better. The latest version of Abyss has the bloom-filter implementation which can run at low memory. It might be practical to check out these two.

ADD COMMENTlink written 2.9 years ago by Rohit1.4k

i think that minia give contigs while i want to assemble in scoffold level but i might check Abyss.

thanks a lot

ADD REPLYlink written 2.9 years ago by reza210

I usually use the SOAP-scaffolder or SSPACE for scaffolding later. Your call though :)

ADD REPLYlink written 2.9 years ago by Rohit1.4k
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