This checklist represents the minimal requirements for installing the OND GridION Mk1 in your institution. For full explanation of requirements, please continue to the document.

The GridION™ is a benchtop device for in vitro diagnostics designed to run and analyse up to five OND Flow Cells.

The GridION benefits from the inclusion of on-board compute which permits data acquisition, analysis and feedback, basecalling, data streaming and device control, all without placing any additional burden on existing IT infrastructure.

All device control, basecalling, analysis and orchestration on the GridION is carried out by pre-installed custom software created by Oxford Nanopore Diagnostics. The default data analysis workflow when using the OND GridION Mk1 is as below:

Figure 1: Default data analysis workflow of the OND GridION Mk1 device

The OND GridION Mk1 is designed around a simple user interface on top of cutting-edge custom electronics providing real-time analysis solutions:

Installing the GridION Mk1 in your institution is similar to installing any new computer. Requirements for the device are as follows:

The two requirements for firewall permissions are: 1. Access to the AWS eu-west-1 region for telemetry feedback and use of the EPI2ME platform through port 443. 2. a. Access to the Linode-hosted IP addresses 178.79.175.200 and 96.126.99.215 for software distribution. b. OR DNS rules ping.oxfordnanoportal.com, mirror.oxfordnanoportal.com, and *.nanoporetech.com

Telemetry information is collected by MinKNOW during sequencing runs as per the Terms and Conditions to allow monitoring of device performance and enable remote troubleshooting. Some of this information is obtained from free-form text entry fields, therefore no personally-identifiable information should be included. No sequence data is collected.

The LamPORE assay analysis produces a number of files that contain sequence data, summary information, and test results.

Nanopore sequencing data is stored in the FASTQ file type. Basecalling summary information is stored in a sequencing_summary.txt file:

• FASTQ is a universal text-based sequence storage format, generated when the nanopore signal data is basecalled and containing both the sequence of DNA/RNA and its quality scores. By default, the device saves up to 4000 sequences in one FASTQ file.
• 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.

The experiment results can be found in the PDF report and the barcode_counts TSV file:

• The TSV file describes the number of reads which align to given targets and have given barcodes. The fields in the TSV file are as follows:

• The PDF report contains classification results for every barcoded sample.

The GridION has sufficient SSD disk space for multiple tests to be carried out. However, it is imperative this data store is cleared regularly in order to prevent successive runs from terminating due to lack of storage space. For this, a site must provide storage to transfer data off the device.

Oxford Nanopore Diagnostics build and provide numerous software types involved in acquisition, orchestration and analysis:

MinKNOW carries out several core tasks:

• Device control, including run parameter selection
• Data acquisition
• Real-time analysis and feedback
• Data streaming
• Basecalling

The MinKNOW software carries out several core tasks: data acquisition, real-time analysis and feedback, basecalling, data streaming, controlling the device, and ensuring that the platform chemistry is performing correctly to run the samples. MinKNOW takes the raw data and converts it into reads by recognition of the distinctive change in current that occurs when a DNA strand enters and leaves the pore. MinKNOW then basecalls the reads, and writes out the data into FASTQ files.

The analysis pipeline:

• Demultiplexes the reads by FIP barcodes that were introduced into the DNA during the Loop-mediated isothermal amplification (LAMP) step of the LamPORE assay
• Aligns the reads against the viral genomic targets
• Generates a TSV file describing the number of reads for each barcode which align to the targets. A PDF report is also generated, containing classification results for every barcoded sample.

Only reads that have had barcodes identified will then be aligned against the SARS-CoV-2 genome. Those samples that align will be noted as positive (SARS-CoV-2 detected) and those where no reads or few reads align will be noted as negative (SARS-CoV-2 not detected).