PC for bioinformatics
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7 weeks ago

Hi everyone!

I'm a beginner in the field of bioinformatics, and planning to go deep. Our lab wants to buy a new PC (mine is also really old). So I thought it would be a nice idea to buy not a common PC, but one with great performance for bioinf. It will be a desktop computer for the lab (not something I can take home). So in case I leave the lab, it will be useful for future students/postdocs doing genomics.

Regarding the work, we are planning of doing analyses of short and long reads (WGS, RNA-seq, ATAC-seq both bulk and single cell). About the money, up to 4K € (more or less). Which do you think is a good deal? Any suggestions? Thank you so much in advance!

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7 weeks ago
d-cameron ★ 2.7k

Any suggestions?

Do you have/can you get access to a HPC system run by your institute/nation? Utilising such a resource will not only give you access to much greater computing power than a single machine but, more importantly, it will be fully supported by qualified IT professionals. There are many aspects to running a bioinformatics compute environment and beginners don't necessarily understand the amount of behind-the-scenes work involved in running an environment. Everything from system administration tasks (who has admin access, network and remote access configuration, operating system version and patching, software installation), to backups (what happens when your storage dies and you lose $30k worth of experimental data?), to data access and retention policies (how long are you going to keep the data for each experiment? who has access to what data under what privacy/ethics restrictions?).

I know it's not the answer that you're looking for, but proper compute infrastructure is important. Also, be aware that there are certain bioinformatics tools (e.g. many de novo assembler) you will be unable to run on a $4k machine because it won't have enough memory. Cloud compute is another option but unfortunately, it's way too easy to accidentally spend $100k because you didn't turn something off.

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7 weeks ago
GenoMax 121k

If your only option is to get a local desktop then read on ... (using core/shared compute resources should always be the first choice, if possible)

There is no definitive answer for this question since your needs will likely change over time. Maximize the RAM that you can get (compromising on the CPU/core count, if you need to) since that is one thing that can be limiting to type of analyses you can do and for which there is no other substitute. If you are not very tech savvy and don't want to deal with individual component makers for any warranty issues then consider buying a pre-assembled workstation from a vendor that can provide single source of warranty support.

Some past threads that should have pointers you can use:

Bioinformatics Workstation Suggestions
Macbook Pro or PC laptop for bioinformatics?
Would this laptop be futureproof for bioinformatics work
Would this laptop be sufficient for small dataset/sequence analysis?

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