running SOAP using 32G RAM

Question

[reza]

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?

[GenoMax]

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.

[Brian Bushnell]

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.

[edrezen]

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

Answer 1

[Rohit]

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.

[reza]

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

thanks a lot

[Rohit]

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