PromethION 2 Solo IT requirements

Overview

The PromethION 2 (P2) Solo device maintains the flexibility associated with PromethION 24 and PromethION 48 devices but in a compact, accessible form. It is designed for small- to medium-sized academic and research labs, as well as core labs and commercial service providers. The P2 Solo delivers the benefits of high-coverage nanopore sequencing to users with lower sample processing requirements (i.e. up to four full-length sequencing runs per week or 200 flow cells per year). Each flow cell has the capacity to deliver hundreds of gigabases of nanopore sequencing data and presents a convenient way to rapidly enable the coverage required for sequencing larger genomes. Additionally, P2 devices allow you to explore applications and projects enabled by high-output nanopore sequencing, before committing to a P24 or P48 device.

The P2 Solo is a sequencing device that requires external compute to run the MinKNOW software. You can plug a P2 Solo either into a GridION or stand-alone computer.

Specifications - GridION

The P2 Solo can use the GridION device as a convenient compute resource – offering plug-and-play compatibility taking advantage of the GPU contained within the GridION to basecall data generated from the P2 Solo. Furthermore, the operating system, SSD and memory are all compatible with the P2 solo out-of-the-box, and engineered to have the optimum amount of compute resources for sequencing.

Item	Specification
1x GridION (GXB02xxx or greater)	GridION is used by the P2 Solo as the compute resource. A GridION Mk1 with serial number GXB02xxx or greater is required to use all basecalling models with a PromethION Flow Cell.
1 Gb/s RJ45 port with DHCP service	Internet connection and long-term data transfer. Details on using networked storage can be found in the GridION data transfer section below.
Networked storage	See below for detailed instructions for additional storage.
1x RJ45 Ethernet cable (cat5e or higher recommended for 1 Gbps)	Internet connection is required to use MinKNOW. Customers require Ethernet connection for data transfer to remote storage (NFS/SMB).
Telemetry feedback	HTTPS/port 443 to 52.17.110.146, 52.31.111.95, 79.125.100.3 (outbound-only access) or DNS rule for ping.oxfordnanoportal.com
EPI2ME analysis	Ethernet: HTTPS/port: 443 TCP access to AWS eu-west-1 IP ranges: http://docs.aws.amazon.com/general/latest/gr/aws-ip-ranges.html
Software updates	HTTPS/port 443 to 178.79.175.200 and 96.126.99.215 (outbound-only access) or DNS rule for cdn.oxfordnanoportal.com
100-240 V 50/60 Hz AC power outlet	AC Mains power required for both P2 Solo and GridION.
1x USB keyboard	USB Type-A keyboard is needed to operate the GridION (I/O on rear of device).
1x USB mouse	USB Type-A mouse is needed to operate the GridION (I/O on rear of device).
1x HDMI or Display Port cable	A Display Port or HDMI cable is required to view the MinION user interface.
1x monitor	GridION currently supports output with a Display Port-compatible monitor. Additionally, a DP-to-HDMI adapter is provided with the original GridION.

Configuring a new computer

Consumer workstations can include desktop towers and high-performance laptops. Workstations can be used if you are comfortable installing the MinKNOW software and do not already have a GridION. The basecalling performance of your setup will depend heavily on your work station and PC specifications.

Item	Specification
Operating System (OS)	Windows – 11 and 10 macOS – Sonoma (14), Ventura (13), Monterey (12) Linux – Ubuntu 22.04 and 20.04
Storage	Recommended specification 8 TB*+ of useable, internal fast SSD storage. *Note if using 2x 4 TB internal SSDs, they need to appear as a single drive to the OS (e.g. using RAID 0). For more information on data sizes, see the information above about storage required for data generated by the P2 Solo.
GPU	Recommended specification NVIDIA GPU with at least 12GB of GPU memory Note: High-end NVIDIA GPUs (RTX 4090 recommended) are recommended for real-time high accuracy basecalling (HAC). MacOS - Mac Studio is recommended for real-time basecalling using the fast model.
Memory	Recommended specification 64 GB of DDR4+ RAM
CPU	Recommended specification 12-core/24-thread Intel i7/i9 10th gen or newer processor / AMD Ryzen processor
Electrical	Consult your workstation/desktop computer manufacturer for electrical specifications. The P2 Solo is powered by a mains supply voltage of 100-240 V 50/60 Hz AC, with a 60 W maximum power draw. Power draw will depend on the sequencing run conditions (e.g. temperature, number of flow cells, etc.) Note: Do not use an extension cord to connect the P2 Solo and the computer.
1x USB-C port	For transferring sequencing data for up to two PromethION flow cells. Designed for a maximum data transfer rate of 5 Gb/s (USB 3.0 or higher). Note: If using a workstation/desktop computer, please ensure you are: - Plugging your P2 Solo directly into the workstation computer's motherboard. - Not using a PCIe to USB-C adapter card (this is known to cause USB communication errors). Failure to plug the P2 Solo directly into the computer motherboard will cause device issues. If your workstation does not have a USB-C port on the motherboard, a USB-C to USB-A cable can be provided upon request. This USB-A port must be a USB 3.0 speed or greater. If your P2 Solo does not appear in MinKNOW, this could be due to an antivirus or endpoint detection and response package. If your IT security policies require such third party software please contact your IT department to ensure the below codes are whitelisted in the peripheral controls of the third party software. Users will be responsible for validating the sufficiency of the applied codes on P2 Solo performance. For more information please visit: How do I connect my P2 Solo?
Telemetry feedback	HTTPS/port 443 to 52.17.110.146, 52.31.111.95, 79.125.100.3 (outbound-only access) or DNS rule for ping.oxfordnanoportal.com
EPI2ME analysis	Ethernet: HTTPS/port: 443 TCP access to AWS eu-west-1 IP ranges: http://docs.aws.amazon.com/general/latest/gr/aws-ip-ranges.html
Software updates	HTTPS/port 443 to 178.79.175.200 and 96.126.99.215 (outbound-only access) or DNS rule for cdn.oxfordnanoportal.com
Operating environment	Consult your computer documentation on operating temperatures. Vents should not be obstructed, otherwise basecalling performance will be affected.

Here is a non-exhaustive list of example models/workstations that meet or can be configured to meet the recommended specification for the P2 Solo. We have not extensively tested any of these computers, so purchasing is at your own risk. Ensure that you have configured the computer to meet the specification in the table above. Other manufacturers are available; check the availability for your region.

Example computers (available as of July 2024)

• Dell Precision 7960 with 2x A6000 GPUs
• Dell Precision 7770
• Dell Precision 3660
• Lenovo - ThinkStation P520/P620 Tower
• Alienware Aurora R16 Desk with RTX 4090 GPU

Telemetry

MinKNOW collects telemetry information during sequencing runs as per the Terms and Conditions to allow monitoring of device performance and enable remote troubleshooting. Some of this information comes from free-form text entry fields, therefore no personally-identifiable information should be included. We do not collect any sequence data.

The EPI2ME platform is hosted within AWS and provides cloud-based analysis solutions for multiple applications. Users upload sequence data in FASTQ format via the EPI2ME Agent, which processes the data through defined pipelines within the EPI2ME Portal. Downloads from EPI2ME are either in Data+Telemetry or Telemetry form. The EPI2ME portal uses telemetry information to populate reports.

Software updates

The IP address from which you receive software updates will depend on your geographical location. You can update through the software UI or through apt on the terminal, so you require outbound-only access. We notify users about software updates through the Nanopore Community and provide full instructions for updating in each release note.

Storage

File types

Nanopore sequencing data is stored in three file types: POD5, FASTQ and BAM. Basecalling summary information is stored in a sequencing_summary.txt file:

• POD5 is an Oxford Nanopore-developed file format which stores nanopore data in an accessible way and replaces the legacy .fast5 format. This output also reads and writes data faster, uses less compute and has smaller raw data file size than .fast5. POD5 files are generated in batches every 10 minutes. The files can be split by barcode if barcoding is used, but splitting by barcode is off by default.
• .fast5 is a legacy file format based upon the .hdf5 file type, which contains all information needed for analysing nanopore sequencing data and tracking it back to its source. A .fast5 file contains data from multiple reads (4000 reads as default), and is several hundred Mb in size.
• FASTQ is a text-based sequence storage format, containing both the sequence of DNA/RNA and its quality scores. FASTQ files are generated in batches by time, with a default of one file generated every 10 minutes. However, you can configure this frequency to 10 minutes, one hour, or one file generated at the end of the run. You can also batch the reads based on the number of reads per file.
• BAM files are output if you perform alignment or modified base calling on the basecalled dataset. BAM file generation options are the same as for FASTQ files. BAM files are off by default and switched on automatically if alignment or modified base calling is used.
• sequencing_summary.txt contains metadata about all basecalled reads from an individual run. Information includes read ID, sequence length, per-read q-score, duration etc. The size of a sequence summary file will depend on the number of reads sequenced.

Example file sizes below are based on different throughputs from an individual flow cell, with a run saving POD5, FASTQ, and BAM files with a read N50 of 23 kb. TMO = theoretical maximum output.

Flow cell output (Gbases)	POD5 storage (Gbytes)	FASTQ.gz storage (Gbytes)	Unaligned BAM with modifications (Gbytes)
100	700	65	60
200	1,400	130	120
290 (TMO)	2,030	188.5	174

As an experiment progresses, POD5 files are produced for all reads. If you choose to basecall your data, these reads are used by the MinKNOW software to generate sequence data which is then stored in FASTQ files and/or BAM files.

Data transfer and long-term storage

It is essential that data is streamed from the device in real-time to prevent runs from terminating due to lack of storage space (this is common for high specification laptops). For this, a customer site must ensure that connectivity to the local infrastructure/external SSD is of sufficient bandwidth to prevent data backing up. We recommend storage presented as NFS or CIFS. To stream data to storage in real-time, SSD is required due to its high write speed compared to HDD. After initial writing to networked SSD drives, data can be moved to storage with a slower write speed for long-term storage.

The form and volume of data to be stored will depend on customer requirements and whether you wish to basecall your sequencing data in the future when more advanced basecalling algorithms are available:

• Storing POD5 files with raw read data in will permit re-basecalling of data when new algorithms are released by Oxford Nanopore Technologies. In such cases, new releases of basecallers have enabled significant improvements in basecalling accuracy of existing datasets through re-basecalling. Further, selected Oxford Nanopore and third-party tools use the raw signal information contained within the POD5 to extract additional information from the raw signal, e.g. calling modified bases, reference-guided SNP calling, or polishing of data.
• Retaining only FASTQ files will allow use of standard downstream analysis tools using the DNA/RNA sequence, but no further sequence data can be generated when improvements in basecalling become available.

Oxford Nanopore is unable to provide exact recommendations for storage, as these will be site-specific. The requirements below should be taken into consideration.

GridION data transfer

If you are using a P2 Solo in combination with a GridION and require additional SSD storage, ensure you are using the correct USB port/Ethernet on the rear of the device. Do NOT use either the USB port with a white, rectangular centre or those at the front of the device (if your GridION has front-facing USB ports).

Instead, use the blue USB Type-A ports on the rear of the GridION (see the image below for reference). Alternatively if using Ethernet, ensure that you are using a cable capable of at least 1 Gbps (CAT5e) and the minimum length for reduced latency.

Support

For more information and FAQs about the PromethION 2 Solo, refer to the P2 Solo self-service page.

Change log

Date	Version	Changes made
31st July 2024	V10	- Renamed "Specifications - workstation/laptop" section to "Configuring a new computer." - Removed minimum specifications for Storage, Memory, GPU and CPU. - Updated recommended GPU to "NVIDIA GPU with at least 12GB of GPU memory. - Added note on GPU recommendations for real-time high accuracy basecalling. - Removed Apple silicon (M1, M2) GPU recommendation. - Added note on P2 Solo not appearing in MinKNOW due to antivirus/endpoint detection packages and how to resolve. - Merged "Example laptops" and "Example desktop" workstation lists to "Example computers" and updated items in list. - Renamed item "100-240 V 50/60 Hz AC power outlet" to "Electrical"; added recommendation to consult manufacturer electrical specifications - Added note not to use extension cord to connect P2 solo and computer. - Added note on operating temperatures of computer - In "File types", updated information about data generation for POD5, FASTQ and BAM files.
24th April 2024	V9	- In "Specifications - workstation/laptop", updated operating system recommendations for Windows, macOS and Linux. - Updated CPU and GPU recommendations to include Apple silicon (M1 and M2)
20th February 2024	V8	- In "Specifications - workstation/laptop", more information has been added about USB-C port requirements. - Minor corrections and clarifications throughout the document
28th September 2023	V7	- A file size table has been added to "File types" - The required operating system for Mac has been updated in "Specifications - workstation/laptop" - Minor corrections and clarifications throughout the document
4th August 2023	V6	A disclaimer has been added to "Specifications - workstation/laptop": "Do not use a USB-C to USB-A adapter to plug the device into your computer, as this can cause issues with connectivity."
28th June 2023	V5	- In "Specifications - GridION" and "Specifications - workstation/laptop", the specs for telemetry feedback, EPI2ME analysis, and software updates have been changed. - In "Specifications - workstation/laptop", the minimum storage recommendations have been updated. - "Networking explanations" has been removed. - In "File types", information has been added about POD5 files and BAM files. The file size comparison table has been temporarily removed. - The "Included software" section has been removed. - A "Support" section has been added - Minor corrections and clarifications throughout the document.
27th February 2023	V4	In "Specifications - workstation/laptop", "1x Type-C port" has been changed to "1x USB-C port"
12th December 2022	V3	- Ubuntu 18.04 has been removed from the workstation/laptop specification table
1st November 2022	V2	- A list of compatible workstations/laptops has been included after "Specifications - workstation/laptop" - In "Specifications - workstation/laptop", the requirements have been updated from 1 x USB TypeA/Type C port to 1 x USB Type-C port.
May 2022	V1	Initial publication