MinION Mk1B IT requirements

Overview

The MinION™ is a small, self-contained device for nanopore sequencing. It plugs directly into a USB Type-A port or a USB Type-C port

with a recommended adapter (5 Gbps).

The MinION device is controlled by the MinKNOW™ software.

MinKNOW carries out several core tasks. These include data acquisition, real-time analysis and feedback, basecalling, data streaming,

device control including selecting the run parameters, sample identification and tracking. Furthermore, it ensures that the platform

chemistry is performing correctly to run the samples.

with the rate of data generation.

Component Required specification: GPU high-accuracy basecalling Required

specification:

data

acquisition/CPU

basecalling

(note: CPU

basecalling

performance is

limited - a GPU is

Linux – Ubuntu

22.04 and 20.04

Memory/RAM 16 GB RAM or higher 16 GB RAM or

higher

CPU Intel i7, i9, Xeon, or better, with at least 4 cores/8 threads

Ryzen 5, 7, or better, with at least 4 cores/8 threads

Apple silicon (M1, M2)

Intel i7, i9, Xeon, or

better, with at

least 4 cores/8

threads

Ryzen 5, 7, or

Technical information can be found on various websites, for example

the RTX 2060 SUPER, RTX 2070, RTX 3060, RTX 3070. Ampere-based GPUs

(the 3000 series, A series etc.) are particularly recommended for optimal

performance.

Apple silicon (M1, M2)

If you are working with a different type of GPU than the models listed above,

please ensure that it has a CUDA Compute Capability >6.1 (for more

information about CUDA-enabled GPUs, see the NVIDIA website).

Storage 1 TB internal SSD or higher 1 TB internal SSD

or higher

(note: CPU

basecalling

performance is

limited - a GPU is

recommended)

We recommend internal solid-state storage for MinKNOW installation as well as data output/acquisition. Solid-state

drives are much faster than traditional hard drives and are able to keep up with the flow of data generated during a

sequencing run.

Computer recommendations

Below are some examples of models/workstations that meet or can be configured to meet the recommended specification for the

Connecting the MinION Mk1B to a computer without a USB Type-A port

If your laptop does not have a USB Type-A port, we recommend using a USB Type-A to USB Type-C adapter (Female to Male 5 Gbps).

Below is a non-exhaustive list of example adapters. We have not extensively tested all models below, so purchasing is at your own

risk.

StarTech 6”

RS Pro 150 mm

Belkin

The below requirements are to ensure correct operation of the MinION during a sequencing experiment:

Component Minimum requirement

User

Local Administrator privileges are needed for MinKNOW installation and updates.

support@nanoporetech.com if you are planning to use your MinION offline.

Antivirus

settings

Antivirus software scanning the entire hard drive uses significant amounts of resources and may

cause performance issues. For this reason, it is recommended that the antivirus scans are switched

to manual setting, rather than to automatic, so that they can be performed when the MinION is not

in use.

OS update

settings

OS system updates should be switched to manual mode, as downloading them during a sequencing

experiment may impact performance.

Updates that require restart will fatally halt a run.

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 cdn.oxfordnanoportal.com

Component Minimum requirement

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.

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

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.

Flow cell output

(Gbases)

POD5 storage

(Gbytes)

FASTQ.gz storage

(Gbytes)

10 70 6.5 6

15 105 9.75 9

30 210 19.5 18

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.

28th June

2023