Hi!
I'n my lab we are interested in buying a new work station and we are looking for suggestions.
We work with NGS data and human genomes so we need a fast machine able to manage loads of big files.
What is "NGS data" and "human genomes", does it mean WGS? What kind of workflows are you running, what what is your budget? For example my work almost exclusively uses single-threaded operations so I bought a workstation with few but fast CPUs, everything else gets outsourced to a HPC. Other analysis types might benefit from massive parallelization, so many CPUs with lower per-core clock speed. Is your analysis memory-intensive, and I/O-intensive? Do you have HPC-like resources available and the workstation is for the analysis that come after the preprocessing (alignment etc)?
I apologize for not being very clear.
I've been asked to do some research but I'm not very computer savvy.
The analyzes we do more often are actually analyzes that come after the preprocessing (alignment etc).
We need a machine that allows us to work with human whole-genome sequencing (WGS) data.
We usually have loads of big files such as FastQ, Bam, gVCF.
Also there are often different people working at the same time.
And is this patient data? And how much is 'loads of big files'? Like in 1 or 100 Illumina runs per week? And do you have an institutional IT department?
Suggestions in this past thread are still valid: Bioinformatics Workstation Suggestions If you already are doing NGS analysis then you have an idea of what your workflow needs in terms of hardware. Ultimately much will depend on your budget and if you need to buy a support contract. Working with local IT support is generally beneficial since you will need to adhere to local security guidelines/practices.
A few points here. Setting up such a compute environment should not be taken lightly and may have legal implications.
Talk to your IT dept. first.
I would not recommend going for a workstation in the sense of a computer you put in someone's office, but a server.
Then let everyone who needs access log in to the server via ssh if that is allowed.
I recommend 128GB of memory and 8-12 physical CPUs as the absolute minimum.
Such server hardware and attached storage creates heat and noise, better not put it in your office, you wouldn't like it.
Think about storage space and backup, how much do you need, can it be easily expanded, how does this integrate into your IT infrastructure and legal framework?
Get legal advice. Human data is often regarded as sensitive data and specific requirements for secure storage, access, and keeping records may apply. That is different from one jurisdiction to another (possibly a bit laxer in US).
You maybe cannot use public cloud infrastructures unless they are certified. If there is a certified cloud solution or HPC provider already, consider using that instead.
Who is going to administrate the resource and keep the OS up to date, apply security patches, etc.?
My prior assumptions on which this is based:
You are doing WGS re-sequencing of whole human genomes for e.g. de-novo variant identification, rare disease analysis etc. in addition RNA-seq and other genomics
These human data are in fact patient data
You have funding that is adequately matched with your project (meaning if you have to do these tasks there is an allocation for funding buying and deprecation of compute and storage resources that will also allow you to do it)
version 2.3.6
What is "NGS data" and "human genomes", does it mean WGS? What kind of workflows are you running, what what is your budget? For example my work almost exclusively uses single-threaded operations so I bought a workstation with few but fast CPUs, everything else gets outsourced to a HPC. Other analysis types might benefit from massive parallelization, so many CPUs with lower per-core clock speed. Is your analysis memory-intensive, and I/O-intensive? Do you have HPC-like resources available and the workstation is for the analysis that come after the preprocessing (alignment etc)?
thank you for your answer!
I apologize for not being very clear. I've been asked to do some research but I'm not very computer savvy. The analyzes we do more often are actually analyzes that come after the preprocessing (alignment etc). We need a machine that allows us to work with human whole-genome sequencing (WGS) data. We usually have loads of big files such as FastQ, Bam, gVCF. Also there are often different people working at the same time.
And is this patient data? And how much is 'loads of big files'? Like in 1 or 100 Illumina runs per week? And do you have an institutional IT department?