Document version Q_GIR_revC_26Sep2024

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

*Size of storage required will depend on use case. Refer to the information below for storage guidelines.

The GridION™ Q is a benchtop device for nanopore sequencing designed to run and analyse data from up to five flow cells. It enables labs operating under regulatory requirements to access the benefits of nanopore sequencing:

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

In addition, the GridION Q also allows users to offer nanopore sequencing as a service when certified.

The GridION Q 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 Q is carried out by pre-installed custom software created by Oxford Nanopore Technologies.

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

Installing the GridION Q is similar to installing any new computer. Requirements for the device are as follows:

The sequencing software collects telemetry information if the GridION Q is connected to the internet. This allows monitoring of device performance and enables 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. If you are running the GridION Q offline and require troubleshooting, you will be able to send telemetry to Oxford Nanopore Technologies via a different route.

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

• FASTQ is a text-based sequence storage format, containing both the sequence of DNA/RNA and its quality scores. By default, nanopore sequencing experiments save up to 4000 DNA sequences in one FASTQ file. File size can vary from <1 Mb to tens of Mb depending on the number and length of sequences.
• BAM files are output if you perform alignment or modified base calling on the basecalled dataset.
• 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.

In addition, sequencing data is available in two other optional file types:

• POD5 is an Oxford Nanopore-developed file format which stores nanopore data in an accessible way. This output also reads and writes data faster, uses less compute and has smaller raw data file size than .fast5.
• .fast5 is a 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.

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.

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

The GridION Q has sufficient SSD disk space for multiple runs to be carried out, storing both FASTQ and BAM 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.

The GridION runs on Ubuntu and can mount multiple filesystem types. We recommend storage presented as NFS or CIFS. The form (and volume) of data to be stored will depend on customer requirements:

• Storing POD5 files with raw read data in will permit re-basecalling of data when new algorithms are released by Oxford Nanopore. 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. modified bases calling, reference-guided SNP calling or polishing of data.
• Retaining just 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.

Can I use an uninterruptible power supply (UPS) with the GridION? Yes you can use a UPS, however we are unable to recommend a specific product.

Do you have any recommendations for how to move data off the GridION in real time during a sequencing run? Currently we recommend moving the data off the box using rsync run hourly through crontab. For further details, please email support@nanoporetech.com