PromethION 2 Integrated (PRO-INT002)

The PromethION 2 Integrated (P2i) is a benchtop device for nanopore sequencing designed to run and analyse up to two flow cells. It is ideal for labs with multiple projects that need the advantages of nanopore sequencing, such as:

• Simple library preparation
• Real-time analysis
• Biological insights from long reads

The device benefits from the inclusion of on-board compute, which enables device control, data acquisition, real-time basecalling, and data streaming, all without placing any additional burden on the existing IT infrastructure. It can also perform post-basecalling data analysis, e.g. using EPI2ME workflows.

Oxford Nanopore Technologies provides pre-installed custom software that carries out all device control, data acquisition and basecalling on the device.

Installation Checklist

This checklist outlines the minimum IT and infrastructure requirements for installing the PromethION 2 Integrated at your institution. For a complete explanation of each item, refer to the sections that follow.

Item/setup required	Purpose
Appropriate length Ethernet cable (Cat5e or greater)	Connection to the IT infrastructure and the internet
1 X 100–240 VAC (50/60 Hz) outlet	Device power
(Optional) Wired USB keyboard and 2-3 button USB mouse	Device control
(Optional) DisplayPort (recommended) or HDMI-compatible monitor Recommended screen resolution: 1920x1080	Device control
(Optional) Uninterruptible power supply (see section 7.1 for details)	Power stability
Sufficient local infrastructure to support storage requirements	Real-time and long-term data storage

Power and UPS requirements

Power reliability is essential for protecting sequencing runs and ensuring stable operation. We strongly recommend using Uninterruptible Power Supplies (UPS) to protect both the PromethION 2 Integrated and any attached display.

Why use a UPS?

A UPS provides backup power and voltage regulation. In the event of a power cut or fluctuation, it can:

• Keep the system running for several minutes
• Trigger alerts that allow sequencing runs to be paused or safely shut down
• Help prevent issues caused by unstable or poor-quality mains power

Recommended UPS specifications

The best option will depend on your site setup, including space, power access, and budget. We recommend consulting your facilities team and/or a qualified electrician to determine the most suitable configuration for your environment.

Parameter	Minimum requirement
Power rating	1.5 kVA
UPS type	Online / double conversion
Transition time	<5 ms
Battery runtime	≥ 5 min (to allow safe shutdown or generator switch-over)
Output type	Pure sine-wave
Output voltage	200–240 VAC @ 50/60 Hz
Power Cables	Ensure cables are rated to a minimum of 10 A 250 VAC, and compatible with the C13 input of the PromethION 2 Integrated

You will need to provide your own UPS. Oxford Nanopore Technologies does not validate or supply specific models. Selection, installation and maintenance are your responsibility.

Installation readiness

• UPS systems must support your region’s voltage, plug type, and circuit protection
• Where possible, install the UPS ahead of system delivery to avoid delays
• Train relevant staff on safe shutdown procedures
• Schedule regular UPS maintenance to ensure continued protection
• Oxford Nanopore Technologies does not cover customer-supplied UPS devices under its support plans

Network and connectivity requirements

Before installing the device, you will need 1 × Ethernet cable (Cat5e or higher) and network access that provides either a DHCP-assigned or statically configured IP address.

Network access requirements

The system uses outbound-only connections over TCP ports 80 and 443 and does not require any inbound access.

Oxford Nanopore Technologies does not have remote access to your system.

Required domains

The table below outlines the domains that must be accessible for specific system functions:

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™ Labs	Access for container-based analysis workflows	*.github.com hub.docker.com
Nanopore account login	To log in to your Nanopore account to access cloud services	id.nanoporetech.com *.okta.com

If your institution uses a proxy or firewall, configure it to allow outbound access to these domains to ensure software functionality, updates, and 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. Avoid entering personally identifiable information in these fields. We do not collect sequence data.

• Install the system on a stable surface with adequate ventilation
• Allow 30 cm clearance to the front, rear and sides of the device
• Place the device in a controlled environment: away from direct sunlight and heat sources to avoid issues with temperature regulation, and in a dust-free area, away from open windows to minimise contamination and airflow issues.
• Connect the UPS to the PromethION 2 Integrated using appropriately rated cables (10 A 250 VAC)
• Follow the installation instructions your UPS manufacturer provides, and consult a qualified electrician where appropriate

File types

The system stores nanopore sequencing data in the following file types:

• FASTQ - A text-based format that stores DNA/RNA sequences and quality scores
• BAM - A format for aligned reads, including modified base calls (e.g., 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)	FASTQ.gz storage (Gbytes)	Unaligned BAM with modifications (Gbytes)	(Optional) POD5 storage (Gbytes)
100	65	60	700
200	130	120	1,400

Note: When basecalling is turned on, the system will create FASTQ and/or BAM files, and will require additional temporary storage while the sequencing run is active. If you elect to turn on POD5 output, the system will generate POD5 files continuously during the experiment.

EPI2ME analysis

The EPI2ME Desktop Application provides user-defined local or cloud-based analysis solutions:

• Local analysis runs directly on the user’s computer, using available compute resources
• The cloud-based analysis runs on Amazon Web Services (AWS) and requires an internet connection

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

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

Software updates

You can download updates via the MinKNOW interface or terminal (using apt). The system only requires outbound access.
We share notifications about software updates through the Nanopore Community and provide full update instructions in each release note.

Data transfer

The P2i has sufficient SSD disk space for multiple sequencing experiments, storing POD5, FASTQ, and BAM data. However, it is imperative to clear this data store regularly to prevent successive runs from terminating due to a lack of storage space. For this, a site must provide storage to transfer data off the device.

The P2i runs on Ubuntu and supports mounting multiple file system types. We recommend using storage presented as NFS or CIFS. The form and volume of data you store will depend on your requirements:

• You can choose to store POD5 files with raw read data or delete them. If you wish to rebasecall your data at a future date, you can optionally save raw POD5 files as a toggle in MinKNOW.
• Retaining only FASTQ/BAM files will allow the use of standard downstream analysis tools using the DNA/RNA sequence.

Estimated transfer times

The table below provides approximate transfer times for different flow cell configurations using 1 Gbps and 10 Gbps connections.

Flow cell configuration	1 Gbps transfer time	10 Gbps transfer time
1 × 200 Gbase flow cell	~7 h	~3 h
2 × 200 Gbase flow cells	~14 h	~6 h

Use this information to assess your site’s bandwidth requirements and plan infrastructure accordingly.

Storage recommendations

To ensure stable data handling and long-term accessibility, consider the following storage strategies:

• Short-term storage Use SSD-based networked storage (e.g., NFS or CIFS) for high-speed streaming during active sequencing runs
• Long-term archiving After sequencing, you can store the data on slower, cost-effective archival storage solutions
• File format considerations
  • Store POD5 files if you plan to re-basecall the data later or use tools requiring raw signal data access
  • Store FASTQ files for downstream analysis if you don’t need to reprocess raw data

Oxford Nanopore Technologies does not prescribe specific storage volumes or architectures, as these requirements vary by site. We recommend working with your local IT team to define:

• Real-time data streaming infrastructure
• Short-term high-speed storage
• Long-term archival capacity

Device identification

Device part number:

PRO-INT002 - PromethIOn 2 Integrated

Intended use

The PromethION 2 Integrated is an electronic analysis platform designed for use in scientific research. Its core technology uses a nanopore to detect single-molecule events, including nucleic acids (DNA/RNA), proteins, and small molecules.

This product is for research use only.

Safety information

• Install the system on a stable surface with adequate ventilation
• Ensure the environment is dust-free, and located away from open windows
• Allow 30 cm clearance to the front, rear and sides of the device

Emergency procedure

In the event of an emergency:

1. Switch off the PromethION 2 Integrated device using the power switch
2. Unplug all power cables from the rear of the device

Declaration of conformity

The PromethION2 Integrated complies with relevant EMC and Electrical Safety directives, as outlined in the EC Declaration of Conformity below.

Declaration of Conformity (DoC) for the PromethION 2 Integrated.

Compliance labels

PromethION 2 Integrated compliance label

License and warranty

The license and warranty contract ensure your instrument performs optimally by providing the latest up-to-date hardware and software. Oxford Nanopore Technologies guarantees the delivery of its support obligations during the contract period, as laid out in sections 4 and 7 of the Nanopore Product Terms and Conditions.

For more information on the device warranty, visit this page on the Oxford Nanopore Store.

How can I transfer data off the PromethION during a run?

The software includes scripts for real-time transfer. For assistance, contact support@nanoporetech.com.

What storage options can I connect?

The PromethION can connect to any NAS. Using the guidance provided above, discuss suitable solutions with your IT team.

Oxford Nanopore Technologies ships PromethION devices in protective packaging. If you notice any damage to the box or signs of mishandling, refuse the delivery and notify Customer Service at support@nanoporetech.com.

We store and ship all systems at ambient temperature (+15˚C to +25˚C).

Please note that the PromethION 2 Integrated is shipped separately from the kits and flow cells.

Shipping container specifications

Component	Weight (kg)	Dimensions (H × W × D)
PromethION 2 Integrated	13.1	30 × 34 × 64 cm

The PromethION 2 Integrated is compatible with all the latest versions of chemistry for PromethION Flow Cells, sequencing kits, and expansions.

This includes compatibility with:

• Flow Cells: PromethION R10 Series Flow Cell (FLO-PRO114M)
  RNA004 PromethION Flow Cell (FLO-PRO004RA)
• Sequencing kits: The PromethION 2 Integrated is compatible with all V14 chemistry kits: ligation, rapid, barcoding, PCR, cDNA, and Direct RNA kits.
• Latest sequencing software: MinKNOW, Dorado Basecall Server
• Downstream analysis tools: EPI2ME (and included workflows), Oxford Nanopore pipelines (MinKNOW-compatible workflows), and custom-developed tools (Nanopore Community developed tools)