Request for Bioinformatics Workstation Configuration for Bacterial Whole Genome Analysis?

Question

[mathavanbioinfo]

Hi,

We are working on bacterial whole genome analysis for 5,000 bacterial samples to screen for antimicrobial genes. I am looking for a bioinformatics workstation suitable for this type of analysis. Please suggest the configuration details. The sample data size is approximately 500MB per sample.

[Dunois]

In addition to what GenoMax has stated, if this workstation is intended to be used only for this one project, you'll be better off renting compute from AWS or some other compute provider rather than provisioning a workstation yourself.

Answer 1

[GenoMax]

This is a periodically asked question and there is no one answer that will satisfy. Mainly because we don't know what your budget is and how you plan to do the analysis. You say 5000 samples but are you going to analyze them serially or together? Will they be available at the same time or will be trickling in at a set number per interval etc.

Here are some past threads to consider:

Lab workstation/bioinformatics PC recommendations
Tower Server configuration for NGS data analysis
New Work Station for the Lab

If you have access to a central compute facility then you should try to use it over a local workstation since it will likely give you access to larger infrastructure. Save you the hassle of administering a local workstation and keeping it secure. You will still need to deal with data/management/backups but you will have to do that with a local workstation as well.