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! :-)