Forum:PC build for Nanopore data analysis
2
0
Entering edit mode
5 weeks ago
stan.aanhane ▴ 30

Hello,

From my department, we are looking at a PC for Nanopore sequencing. Unfortunately, because we are not entirely at home in the computer world, it is difficult for us to estimate what we need. That's why I'm asking for your help.

The nanopore sequencing itself has no special requirements. These are also neatly supplied by Oxford. We are building a pipeline for the data that is subsequently generated. The PC should also be able to handle this pipeline. We will make a pipeline to complete metagenome analysis to determine specific correlations between microbiome in different conditions. This will be done in python. All our question now is, what are the minimum/ideal specs of the PC. Could you help us with this?

If you have any additional questions, please let me know!

I really appreciate any help you can provide!

Best,

Stan

python PC pipeline nanopore-sequencing • 471 views
ADD COMMENT
0
Entering edit mode

An NVIDIA GPU is necessary if you want to complete the basecalling in a reasonable amount of time. Depending on the budget, any NVIDIA GPU with a cuda compute capacity of 6.1 or higher should works fine

ADD REPLY
0
Entering edit mode

An NVIDIA GPU is necessary

only if software can take advantage of it. Not every tool out there is GPU-capable.

ADD REPLY
2
Entering edit mode

ONT basecallers are performant only with GPU's.

ADD REPLY
0
Entering edit mode

I assumed that this was already covered because of the mention of

a pipeline for the data that is subsequently generated

ADD REPLY
0
Entering edit mode

Thank you, I am aware of this. As stated in the post, the requirements for the MinION are provided by oxford. Its mainly the amount of performance we need for the pipeline we are building, which would be mainly RAM and CPU power.

ADD REPLY
3
Entering edit mode
5 weeks ago
GenoMax 117k

I assume you are referring to MinION sequencing since other larger ONT sequencers are supplied with built in compute for doing some of the initial basecalling etc. See this post for recommendations for hardware when using MinION.

ADD COMMENT
1
Entering edit mode
5 weeks ago

It really depends on the details of your workflows and whether you'll need this computer for other things. You could look at papers describing similar workflows, some report the compute environment used for testing, e.g. the paper Assembly methods for nanopore-based metagenomic sequencing: a comparative study reports running all methods on a computer with CPU: AMD RYZEN 7 1700X 3.4GHZ; Cores: 8; Threads: 16; RAM: Corsair Vengeance 64 GB; SSD: Samsung 860 EVO Basic SSD 500 GB.
If you have access to an HPC this might be a preferable solution.

ADD COMMENT
0
Entering edit mode

We are not done with the details yet. But the current steps are; Base-calling (guppy) -> classification -> Alignment control, and from there, we are still debating how we want to determine correlation. We expect large datasets of around 50Gigabases. The budget is relatively high, at about $10.000. We are currently looking into: AMD Threadripper 3970X (32 cores), 256 GB of ram, and an RTX 3090. But we want to be sure it's enough. But looking at literature, it should be sufficient.

ADD REPLY

Login before adding your answer.

Traffic: 2103 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6