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

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

rna-seq next-gen assembly blast
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updated by Ram Ram • written by seta seta

1 answer

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 ...)

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updated by Ram Ram • written by Nicolas Rosewick Nicolas Rosewick

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?

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updated by Ram Ram • written by seta seta

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

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updated by Ram Ram • written by Nicolas Rosewick Nicolas Rosewick

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.

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updated by Ram Ram • written by seta seta

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