Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore Sequencer

Question

[satrio]

Apple M1 for sequencing and base calling in MinION M1kb Nanopore Sequencer

Has anyone tried using Apple M1 for sequencing and base calling on Mk1B instrument?

We are currently preparing a simple computing device for oxford nanopore sequencing and base calling. Based on the guide on the web https://community.nanoporetech.com/requirements_documents/minion-it-reqs.pdf, OSX can be used for data acquisition especially for CPU basecalling, but it seems to be for devices using intel processors. With the apple silicon M1, what about the compatibility with Mk1B?

Our device: Macbook Pro M1 2020, Memory 8 Gb

Answer 1

[Christopher]

I'm using a Mac Studio with M1 Ultra chip to sequence with a MinION Mk1B now and it's working great! Fast basecalling and adaptive sequencing keeps up with the flow cell reads almost perfectly. Only just starting to run high quality and modified base calling separately on the machine, but also seems good. We started out with Guppy and only just updated to Dorado and it all seems to work well.

[GenoMax]

dorado can't demultiplex data as yet (v.0.3.4). Also no adapter trimming. So something to keep in mind if you are switching.

To address the "no adapter trimming" does anyone have a current recommendation for a nanopore specific adapter trimming tool?

[ATpoint]

Wondering why investing all that money for such an overpriced piece of hardware. You could get an equivalent Windows or Linux workstation for a fraction of the price.

General audiance see also Laptop specs for MiniON

[Ram]

I don't think they bought the Mac Studio just for the MiniON. If they did, that might be overkill. All things considered, I'd prefer an Apple machine over a Windows or Linux workstation with the same hardware - Apple's build just works better. Of course, when budget is a concern, things change.

Answer 2

[cfos4698]

I'm not sure about "legacy" basecalling with guppy, but the newer basecaller dorado, which is still officially in pre-release, can run on M1/M2: https://github.com/nanoporetech/dorado