how many RAM and CPU are required to perform comprehensive NGS analysis?

Question

[seta]

Hi all,

Please provide me how many RAM (GB) and CPU are required to perform de novo transcriptome assembly for about 400 million paired-end reads (using trinity) and subsequent analysis, especially BLAST, which need really powerful computer system? Thanks for any suggestion

Answer 1

[Nicolas Rosewick]

From Trinity website: 1G RAM per 1M ~76 base Illumina paired reads, but often much less memory is required

so 400Gb (that seems a lot ...)

[seta]

Hi friend,

Thanks for your comment, what about CPU, my big concerns is to do blast as fast as possible, how many CPU is required for this purpose?

[Nicolas Rosewick]

It depends on how many sequences you have to blast, and the size of the blast db

[seta]

It's about 43000 contigs derived from transcriptome assembly, that should be subjected to blastx at NCBI as one of tools to evaluate the quality of assembly.