Laptop specs for MiniON

Question

[ve9]

I noticed the minimum requirement below.

I have in the lab this one - Intel Core i7-8565U (8MB Cache), 16GB 2666MHz DDR4, 256GB M.2 PCIe NVMe SSD, AMD Radeon 520 with 2G GDDR5

Does anyone knows if the 1TB SSD is a must? We plan to try sequence a bacterial genome (no barcoding) just plain DNA seq. Also sometimes I see requirement for Nvidia card....so I'm a bit confused. I will appreciate any info from you guys that have experience?

[GenoMax]

We plan to try sequence a bacterial genome (no barcoding) just plain DNA seq.

Do not take this comment the wrong way. While it is tempting to do the sequencing yourself (especially since ONT offers a low entry price for the sequencer) if you intend to do just one genome (or a few, not something you plan to do regularly) then consider using a sequence provider instead. You will save a lot of headache, have data in hand quicker and be on your way to do science.

You may need to worry about hardware to analyze the data (that laptop may not be enough).

[ve9]

We plan to to Illumina also, the Nanopore is just a test drive for a local lab project.

[GenoMax]

Then simply find a sequence provider that will do both types of sequencing and start planning for data analysis.

[joe]

Nanopore has detailed workflows (both sample prep and computational pipelines) which will give you a better indication. Many nanopore workflows use functions that will crunch numbers on cpu or gpu, and most always you want to use the gpu if your'e able. The nanopore in my lab is connected to a desktop with 'nice' specs and even so we do all the number crunching on a cluster. The nanopore software itself has several run modes and you might be limited in which modes you can use if the computer can't support. WRT the SSD, I guess it's recommend/required because of the intense i/o

tldr; you need to understand the requirements of the workflow you plan to follow.

[ve9]

Thanks. Is it possible to check with the software on the PC if the workflow will run properly beforehand (before we got the MiniON)?

[joe]

There is a slightly more detailed brochure by ONT below, and you can google around to find the commands you'd use to process outside of the ONT software, but as others have pointed out it could be 'painful' to work with an underpowered computer/filesystem.

https://community.nanoporetech.com/requirements_documents/minion-it-reqs.pdf

Answer 1

[colindaven]

Basecalling will take forever (days to weeks) if you don't have an Nvidia video card to use with the guppy basecaller. Maybe another group or your local cluster already has this all set up, so ask around.

You can probably use a 0.5 TB SSD just fine.

Calculate the coverage on the fly of the reads you generate to avoid overkill = too much coverage (perhaps 1-3 hours is enough). There's no need to run a modern flowcell for 48 hours to generate data for 1 bacterium, with barcoding 10+ is possible.

[ve9]

Can I just run Minion only sequencing on the laptop I cited above. Can i do the basecalling later on a more powerful computer (also to test different basecaller)? This way i will not need a laptop with Nvidia?

[ve9]

PS can you give a link with info how to calculate this time wich will be enough for a bact genome?

[colindaven]

This coverage link looks alright : https://www.ecseq.com/support/ngs/how-to-calculate-the-coverage-for-a-sequencing-experiment. Just ignore clusters and the pairs, thats for Illumina.

Yes, just transfer the fast5 files to another computer with a GPU. We generally used to run minions without basecalling and use another machine later.