Question: Buy PC for metagenomics
gravatar for lugonauta
10 days ago by
lugonauta0 wrote:

Hi everyone,

I'm new in bioinformatics. I'm working in a clinical microbiology laboratory, and my chief wants to stablish a sequencing department for clinical and research purposes (whole genome sequencing for studying outbreaks, 16s metagenomics for studying microbiota, etc). We want to buy a desktop PC to do all this kind of bioinformatic analysis. For now, I'm using a VM in a laptop with W10, 8GB RAM, 512 GB SSD and Intel Core i7 7gen processor. I faced some memory issues in certain pipelines I run, and it´s time to move to a more powerful machine. Which specifications could you recommend me? I feel confident using a linux-VM in Windows, so I don't want to buy an apple/IOS machine for now.
I have read in other forums that It will be enough 16-32 GB of memory and 1-2 TB of storage...I'm scary about buying something that later doesn't fit our department needs.

I would appreciate your advise ;)

Thanks in advance!

ADD COMMENTlink modified 10 days ago by jrj.healey4.8k • written 10 days ago by lugonauta0

Can you give some more details on the scale of what this department is going to be. Is it some smaller experiments from time to time or is this planned to be a facility that serves an entire hospital and external collaborators? Also, do you or anybody in the department has experience in handling and administrating large-scale sequencing projects and data volumes? Also, is there the hardware for secure backup of raw data?

ADD REPLYlink written 10 days ago by ATpoint5.5k

Hi, sorry about not be as concrete as I should. Our goal is to support the needs of our clinical microbiology laboratory, therefore we would not have a constant activity on a large scale. None of us have broad experience in bioinformatics nor NGS (we about to finish the residency training program in clinical microbiology). Actually, our service doesn't have a DNA sequencer (we outsource the service). We only want to analyze raw sequencing data, in order to not to have to outsource the analysis too. We think it would be enough to buy one powerful computer to start...we can´t afford to build a workstation/cluster for now and we don't have enough informatic knowledge to do so.

ADD REPLYlink written 10 days ago by lugonauta0

I think you are getting a bit confused between IT requirement and bioinformatics here. It would be better to speak to someone in the local IT team who would be presumably managing the system you are going to purchase. They would be able to advise you on the data handling and backup strategy and solutions. It would also help if you would provide them with details about approx size of the data being produced/analysed per year. It is a pure infrastructure/IT based questions and it is not possible for many of us to address such specific questions on this forum.

ADD REPLYlink written 10 days ago by Sej Modha3.1k
gravatar for Sej Modha
10 days ago by
Sej Modha3.1k
Glasgow, UK
Sej Modha3.1k wrote:

Hi There,

I'd suggest that you look at previous threads related to this question on the forum as it should give you an idea about the specification that you might want to go for within available budget.

Computer specs for Bioinformatics

Hardware requirements for NGS analysis

Hardware Suitable For Generic Nextgen Sequencing Processing?

Workstations For Ngs Analysis?

ADD COMMENTlink written 10 days ago by Sej Modha3.1k
gravatar for jrj.healey
10 days ago by
United Kingdom
jrj.healey4.8k wrote:

Getting your hands on as much RAM as you can will be the killer as others have said.

You will really want to look toward buying a "Workstation", rather than a desktop PC, since you will eventually find yourself needing closer to server grade components I suspect. A workstation is not necessarily the same as a server, so fulfils a happy medium I think.

Also, I'd strongly recommend just taking the plunge and getting a proper linux machine set up. VMs add overheads to your computation.

In terms of storage, I would also go quite big on this from the start. Hard drives are dirt cheap (not to mention a single even consumer grade hard drive is inching toward the 8-10Tb mark now).

It would probably be helpful if you could tell us your budget though.

ADD COMMENTlink written 10 days ago by jrj.healey4.8k
gravatar for apaytuvi
10 days ago by
apaytuvi10 wrote:

It depends on what you want to do. In case you want to perform Whole Genome Sequencing metagenomics or metatranscriptomics, you would need quite a lot of RAM memory (specially for Kraken and CLARK), I would say more than 64Gb. It always depends on the pipeline used, megablastn + MEGAN is a slow approach but needs less memory (with 16-32Gb would be enough). Also, if you plan to sequence a lot, you might have a shortage of disk-memory with only 2Tb.

An alternative would be to use online tools to get the data analyzed, such as Gaia (Demo).


ADD COMMENTlink written 10 days ago by apaytuvi10
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