Question: Help w. workstation specs for human exome-seq/variant calling and microarrays? Cores vs speed, RAM
gravatar for mismis
3.7 years ago by
Heidelberg, Germany
mismis0 wrote:


we are currently planning a project that is going to involve exon sequencing as well as microarrays for expression and methylation analysis and I am looking for advice for the hardware side of things.

Even if final analysis would run e.g. on external servers, we still need a workstation for general bioinformatics and toying with ideas and implementations.

One thing that I really would appreciate getting comments on is the balance between clock speed and number of cores in Xeon processors in bioinformatics- I got the impression that most software is not exactly well-suited to multithreading and especially R packages are mostly one-thread-only?

At the moment I am looking at a HP Z440 with these specs: Xeon E5; 3.7 GHz; 4 cores 64 GB RAM 256 GB z-Drive SSD (maybe doubled in a mirror configuration) 3x 3 TB SATA HDDs (three-way-mirror, ZFS)

I am also thinking about going with a Z640 which would be able to hold 256 GB of RAM (compared to the max. of 128 GB with the Z440) and I am not sure about processor choice; it's been a decade since I last followed hardware trends more closely so I know next to nothing about the performance differences in different Xeon versions.

The configuration above is around 4000 EUR / 4200 USD list. Personally I imagine I could find better offers or would buy used but the buying department has some specific vendor contracts... so it most probably will be some new HP workstation.

Long story short: Do I need more cores? Should I get 128 GB RAM initially?

Thank you so much in advance! :-)

exon-seq hardware microarrays • 1.4k views
ADD COMMENTlink written 3.7 years ago by mismis0

Simply put there is no substitute for lack of RAM. If you don't have enough, you can't run that particular analysis. So consider getting an adequate amount that would serve you for next 2-3 years before worrying about cores.

Also getting a CPU a few levels down in the pileup (in terms of speed/cores/cache) would save you a significant amount of money (which you can put towards more RAM). This would add (even if it does add an hour, when something runs overnight you don't worry about it) to the job completion time but would give you the best return for your euros.

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by genomax90k
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