DENOVO ASSEMBLY

Question

[askari.arezou94]

Hi guys I have a serious problem with my data I want to do the Denovo assembly genome with size genome(AFTER TRIMM):2.6 GIG and coverage of 10 of Buffalo. My server ram is 132 Gig and I can't use another server with the highest ram. When running the script I receive a ram space error.

What should I do about this problem?

How can make smaller this genome?

How can do Denovo assembly with 132 GIG ram?

Answer 1

[Carambakaracho]

Dear Arezou, irrespective of the assembler (which you don't mention), I fear your RAM will limit your success. In addition for a denovo assembly of a mammal genome, 10x coverage might be a bit on the low end, the result might disappointing, though there's more qualified people on this forum.

Instead I'd recommend remapping to an existing assembly, which likely yields more success. Still you can try to reassemble the unmapped reads, just in to sure you didn't miss something crucial. Make sure to quality control those reads, so you don't assemble mostly low quality sequence.

[askari.arezou94]

Thank you for the good explanation.

Answer 2

[colindaven]

10X coverage is too low for a good assembly, especially if just illumina reads (but you didn't say what data you have or what assembler you tried).

If you really want to go ahead, you can try minia or soapdenovo. Those are AFAIK fairly low RAM assemblers.

[askari.arezou94]

Tnx for your response. I just have Ilumina reads.