Computer hardware

[mplace]

Our lab is getting ready to purchase a server to do Next Gen Seq analysis.

Do to the cost difference, between AMD & INTEL, we are leaning toward
AMD.

Does anyone have any reason why we shouldn't choose AMD over INTEL?

FYI, the box will be 4 processors, 512 GB ram, 20+ TB of disk space.

Thank you for the suggestions.

[GenoMax]

Our lab is getting ready to purchase a server to do Next Gen Seq analysis.

Do to the cost difference, between AMD & INTEL, we are leaning toward
AMD.

Does anyone have any reason why we shouldn't choose AMD over INTEL?

FYI, the box will be 4 processors, 512 GB ram, 20+ TB of disk space.

Thank you for the suggestions.

This type of advice is asked on SeqAnswers often and in your case you already have an idea of what you want. Ultimately you are the best judge of your group needs.

The Intel/AMD choice is a non-issue (except from the cost perspective that you alluded to). Choosing AMD CPU's would perhaps lead to more heat generation/power needs but with a single server it is not a big problem.

Depending on how much sequencing you are planning to do 20 TB of storage may not amount to a lot (specially if you are going to deal with raw data from illumina). You should also be planning to use some version of RAID (5 or better), so take into account "usable" storage space (after RAID) rather than total disk when doing your calculations.

It is tempting to buy the biggest/fastest server but it may be worth thinking about the kind of analyses (alignments, assemblies) you are planning and throughput (samples/week) you expect to maintain. If you are not planning to do de novo assemblies of large genomes, 512G RAM may be overkill. Money that could be put towards more storage/a data backup solution. The latter is perhaps easy to overlook in the planning phase.

[rhinoceros]

FYI, the box will be 4 processors, 512 GB ram, 20+ TB of disk space.

Thank you for the suggestions.

I do next gen seq analysis on a ~20 node cluster with 16-32 cores and 512-756GB RAM in each node and some algorithms can nevertheless run for days. Point is that there's no general rule to what computer hardware is right as it completely depends on what it's for. As to AMD vs. Intel, I don't think things like this matter unless you're building a big cluster and energy consumption becomes a significant factor..