Computer equipment for metagenomic analysis

Question

[Erin]

Hello everyone,

I am an undergraduate in a lab that does a lot of 16s amplicon sequencing. My lab does a lot of stuff with microbial source tracking and soil microbiome. For years, we have been doing analysis with the Ribosomal Database Project. RDP recently shut down, so we have to completely shift are ways (probably should have been done a while ago).

My PI and have been trying to figure some stuff out to go forward with the research. I have some experience with Linx in a Ubuntu server and I've done some work with Bioconda packages and such. I have no issue with learning that stuff however I am not technically savvy with the computer side of stuff (memory, RAM, all that stuff). I did all my work on an established Ubuntu server.

I'm not sure about the memory size on the new MAC the lab just got but I do know that the MAC has 8 Core processors (pretty low for doing metagenomics). Do you have any advice on where to get started equipment-wise to start doing metagenomic analysis at a relatively fast speed? We are probably switching to either full amplicon or shotgun sequencing. Any advice on how to start with a linux server such a Ubuntu? Recommendations for external drives and other stuff we should purchase before starting a heavy work load.

Answer 1

[ATpoint]

Your PI certainly has a collaborator network that does similar analysis. Ask them what they use and then buy this, don't reinvent the wheel. Especially as an undergraduate your job is to learn how to do science, not to figure out and establish the labs IT infrastructure. That takes time and has no scientific reward at all. Don't fall into that trap!

Answer 2

[colindaven]

Before going it alone you might want to talk to your local HPC infrastructure people.

There are a lot of posts on here on this topic, eg Lab workstation/bioinformatics PC recommendations

You can best access these by google in my experience eg https://www.google.com/search?q=buying+computer+bioinformatics+lab&oq=buying+computer+bioinformatics+lab&aqs=edge..69i57j0i546l3.11525j1j1&sourceid=chrome&ie=UTF-8

Remember, RAM is more important than CPU, and AMD Ryzen CPUs offer great performance. 64 GB RAM would probably be a bare minimum. SSD is also critical - the more the better, min 4+ TB.

For backups you can look at the cloud, eg amazon deep glacier, and or at a local NAS which uses redundant hard disks in a RAID system so your backup is more secure.