The MinION™ Mk1D is a compact, portable nanopore sequencing device designed to bring sequencing to the sample. It must be connected to a computer for power and sequencing control is via the MinKNOW™ software.

MinKNOW manages key sequencing tasks, including:

• Data acquisition and real-time analysis
• Data streaming and device control
• Run parameter selection
• Sample identification and tracking

In addition to collecting raw nanopore signal data, MinKNOW includes a basecalling algorithm that converts this signal into DNA or RNA sequences using machine learning.

This document provides guidance for selecting a compatible computer to run the MinION Mk1D.

Important: The MinION Mk1D requires MinKNOW version 24.11.10 or later.

The specifications below ensure your computer can efficiently acquire data and perform basecalling. Using an unsupported computer may lead to reduced performance, slower basecalling, or failed runs.

Recommended

The recommended specification ensures real-time, high-accuracy basecalling, including detection of modified bases (CpG-context 5mC/5hmC), alignment, and adaptive sampling. This level of performance also supports the generation of super-accurate basecalls in real time.

Minimum

The minimum specification is designed to balance performance and cost. It enables high-accuracy basecalling, with data ready for use at the end of a typical 72-hour sequencing run.

Limitations of the minimum specification:

• Real-time performance may not be achievable for shorter runs or more intensive analytical tasks.
• Adaptive sampling and high-accuracy basecalling may not run simultaneously.
• Super-accurate (SUP) basecalling may require significant additional processing time after a run completes.

Component	Minimum	Recommended
Operating system	Windows 10/11 Ubuntu 22.04/24.04 LTS MacOS	Windows 10/11 Ubuntu 22.04/24.04 LTS
Peripheral	USB Type-C (USB 2.0 or higher)	USB Type-C (USB 2.0 or higher)
Memory	16 GB + Apple: 24 GB + Unified Memory	32 GB +
GPU	NVIDIA RTX 4070 + Apple: M4 Pro +	NVIDIA RTX 4090
CPU	Intel I5 + / AMD Threadripper + / Apple M4 Pro + (6-cores +)	Intel I7 + (12-cores +)
Storage	1 TB SSD +	2 TB SSD +

Note: Compatibility and performance on newly released hardware, such as next-generation GPUs or processors, may be limited until testing and optimisation are complete.

Processor Compatibility

• MinKNOW is only supported on Intel, AMD, and Apple silicon processors.
• Intel-based Macs are not supported.
• Other processors, such as Qualcomm Snapdragon and ARM-based chips are not supported.

USB Connectivity

The MinION Mk1D must be connected to a computer via its USB-C port. It only requires USB 2.0 data transfer speeds, so all USB-C ports capable of data transfer are compatible.

• USB-A to USB-C adapters or cables are not supported, as USB-A ports may not provide sufficient power.

Nanopore sequencing data is stored in the following file types:

• FASTQ - a text-based format that stores DNA/RNA sequences along with quality scores.
• BAM - a format for aligned reads, including modified basecalls (e.g. for methylation).
• sequencing_summary.txt - contains metadata for all basecalled reads from a sequencing run. This includes details such as read ID, sequence length, per read Q-score, and read duration. The size of a sequence summary file will depend on the number of reads sequenced.

Optional:

• POD5 - the primary raw data format replacing the legacy FAST5. It is more efficient in both storage and processing.

The Table below provides estimated storage requirements based on different sequencing throughputs from a single flow cell. These values assume a run that saves POD5, FASTQ, and BAM files, with a read N50 of 23 kb.

Flow cell output (Gbases)	POD5 storage (Gbytes)	FASTQ.gz storage (Gbytes)	Unaligned BAM with modifications (Gbytes)
10	70	6.5	6
15	105	9.75	9
30	210	19.5	18
50	350	35	30

Note: During sequencing, POD5 files are continuously generated. If basecalling is enabled, FASTQ and/or BAM files will be created, and POD5 writing may be disabled however, additional temporary storage will be required.

Network access is required for correct functionality and system updates. All connections are outbound only over TCP ports 80 and 443. No inbound access is required.

Oxford Nanopore does not have remote access to your system.

Access type	Purpose	Required domains
Telemetry	Enables MinKNOW to run and communicate telemetry	ping.oxfordnanoportal.com
Software and OS updates	Access to MinKNOW updates, OS packages, and GPU drivers	cdn.oxfordnanoportal.com *.ubuntu.com *.nvidia.com
EPI2ME	Access for container-based analysis workflows	*.github.com hub.docker.com
Nanopore account login	Required to log into your Oxford Nanopore account and access cloud services	id.nanoporetech.com *.okta.com

Note: If your institution uses a proxy or firewall, ensure outbound access to these domains is permitted to avoid issues with software functionality, updates, or user authentication.

Telemetry

MinKNOW and EPI2ME™ collect telemetry data during use, as outlined in our Terms and Conditions. This helps monitor device performance, supports troubleshooting, and enables flow cell warranty replacement where applicable.

Privacy note: Some telemetry fields allow free text entry therefore, avoid entering any personally identifiable information. We do not collect any sequencing data.

EPI2ME analysis

The EPI2ME desktop application provides user-defined local or cloud-based analysis solutions:

• Local analysis runs directly on your computer, using available compute resources.
• Cloud-based analysis is hosted on Amazon Web Services (AWS) and requires an internet connection.

Find out more about how EPI2ME can support your data analysis needs.

Data upload formats: FASTQ, BAM, and other relevant workflow formats are uploaded through EPI2ME, which processes data via custom Nextflow pipelines and provides interactive HTML reports.

System behaviours such as scheduled updates, antivirus scans, or managed IT policies can interfere with sequencing runs.

Below are some key areas to review and discuss with your IT department to ensure a smooth and uninterrupted sequencing experience.

Component	Minimum requirement
User account privilege level	Local Administrator privileges are required for installation and updates. They are not required for running sequencing experiments.
Internet connection	A stable internet connection is required at all times for software updates and telemetry. For offline use (e.g. fieldwork or expeditions), contact support@nanoporetech.com for guidance.
Antivirus settings	Antivirus software can consume significant system resources, potentially affecting sequencing performance. To avoid disruptions, we recommend disabling automatic scans and scheduling manual scans when the MinION is not in use.
OS update settings	Set OS updates to manual mode, as updates downloading during a sequencing run may cause issues. Updates requiring a restart will halt an active run. Please coordinate with your IT department to ensure that Group Policies do not override local settings in a way that could cause unplanned updates or restarts.
Endpoint detection software	Endpoint detection software may interfere with system performance. We recommend disabling such software during sequencing.
BIOS/chipset settings and updates	Ensure your BIOS firmware and chipset drivers are up to date. For EPI2ME analysis, ensure virtualisation is enabled.

1. Can I use a computer that differs from or is older than the specifications listed here?

Yes, but performance, especially basecalling speed, may vary depending on the hardware. The choice of GPU has the greatest impact on performance.

Hardware compatibility

Older hardware:

• Computers released before 2015 are unlikely to work.
• Ensure your GPU supports Compute Capability 6.1+ (e.g. RTX 10XX series or newer).
• Ensure your CPU supports AVX2 (e.g. Intel Haswell, AMD Steamroller or newer).
• A USB-C port (USB 2.0 or higher) is required for device connection.

Newer hardware:

• Compatibility and performance on newly released hardware, such as next-generation GPUs or processors, may be limited until testing and optimisation are complete.

2. I bought a computer based on a previous version of this document. Is it now obsolete?

This document is intended to guide you when purchasing a new computer for use with the MinION Mk1D. As hardware availability changes over time, we update our recommendations to reflect current, readily available components. If your existing computer still meets the specifications listed in question 1 above, it remains compatible with our software.

3. I want to basecall my data on another computer / HPC. What is the true minimum specification for data acquisition only?

For data acquisition only (sequencing without any basecalling), the minimum specification (excluding the GPU) is sufficient.

4. Can I use Linux distributions other than Ubuntu 22.04/24.04 LTS?

We recommend using only Ubuntu 22.04 or 24.04 LTS. Other Linux distributions have not been tested or validated and may not be compatible with our software or support processes.

5. Why is there no recommended specification for Mac?

While Apple silicon is supported, sequencing performance, especially for resource-intensive models like super accuracy (SUP), is better on systems with NVIDIA GPUs, which also offer a more favourable price-to-performance ratio for basecalling.

For more information and FAQs about the MinION Mk1D, please refer to our devices page on Support.