[BioC] Computer for the analysis of high-throughput genomic data

[Steve Lianoglou]

Hi,

On Thu, Dec 27, 2012 at 11:14 AM, Capurro, Alberto  (Dr.)
<ac331 at leicester.ac.uk> wrote:
> Hello,
>
> I would need to purchase a desktop computer for the analysis of high-throughput genomic data using R/Bioconductor. I want to ask you the specifications that I should look for (as for example ram memory, processor type, number of cores). Can you mention specific examples of state of the art machines fitted for this purpose?

This is a hard question to answer.

Is the machine for yourself, or a lab, more users?

What types of analysis will you be doing? Will you be working with raw
NGS data -- if so, just sequence alignment, assembly, etc? Do you have
a compute cluster to push those types of jobs over to?

Anyway -- absent any of that information, for us mere mortals who shop
at "pro-sumer" levels, I wouldn't complain too much if I had, say, a
12 core, 32-64gb ram osx or linux machine sitting underneath my desk.

If you're working w/ NGS data, no matter how much HD space you get,
you will always run out, so you will constantly have to be adding
upgrades there, but start with several terabytes ... also ... you'll
have to think about how you plan to backup your data, but I'll leave
that as another topic.

But, as I said, the more (of everything) the merrier.

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact