GridION Mk1 IT RequirementsGridION Mk1 IT Requirements
ChecklistChecklist
This checklist represents the minimal requirements for installing the GridION in your institution. For full explanation of requirements, please continue to the
document.
Item/setup requiredItem/setup required ReasonReason Provided?Provided?
1x 1 Gbp/s RJ45 port with DHCP service running Connection to IT
infrastructure and internet
1x 1 Gbp/s Ethernet cable Connection to IT
infrastructure and internet
HTTPS/port 443 TCP access to AWS eu-west-1 IP ranges listed at
http://docs.aws.amazon.com/general/latest/gr/aws-ip-ranges.html
Telemetry feedback,
EPI2ME analysis
HTTPS/port 443 and HTTP/port 80
TCP access to Linode-hosted IP addresses 178.79.175.200 and 96.126.99.215 for
software distribution
OR DNS rules ping.oxfordnanoportal.com, mirror.oxfordnanoportal.com, and
*.nanoporetech.com
Software updates
USB mouse Device control
USB keyboard Device control
HDMI- or DisplayPort-compatible monitor Device control
Power supply capable of delivering 650 W GridION power
Storage: Sufficient infrastructure for required storage option* Long-term data storage
*
Size of storage required will depend on use case. Please refer to the information below for storage guidelines.
GridION Mk1 deviceGridION Mk1 device
OverviewOverview
The GridION is a benchtop device for nanopore sequencing designed to run and analyse up to five MinION or Flongle flow cells, or a combination thereof. It is
ideal for labs with multiple projects that need the advantages of nanopore sequencing:
Simple library preparation
Real-time analysis
Biological insights from long reads
In addition the GridION also enables users to offer nanopore sequencing as a service when certified.
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
Technologies. The default data analysis workflow when using the GridION Mk1 is as below:
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GridION Mk1 IT requirements
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countries. © 2008 - 2021 Oxford Nanopore Technologies. All rights reserved. Registered Office: Oxford Science Park, Oxford OX4 4GA, UK | Registered No. 05386273 | Privacy Policy
Figure 1: Default data analysis workflow of the GridION deviceFigure 1: Default data analysis workflow of the GridION device
SpecificationsSpecifications
The GridION Mk1 is designed around a simple user interface on top of cutting-edge custom electronics providing real-time analysis solutions:
ComponentComponent SpecificationSpecification
Operating system Ubuntu 16.04 running off Intel CPU
Customers are advised to keep up to date with all software and security
patches
Storage 4 TB internal SSD
GPU cards 1x Nvidia Volta GV100
Memory 64 GB RAM
Size and weight H220 x W365 x D370 mm
Weight 11 kg
Environmental ranges Designed to sequence at +18° C to +25° C*
*
Functional range of electronics -5° C to +40° C
Site requirementsSite requirements
Installing the GridION Mk1 in your institution is similar to installing any new computer. Requirements for the device are as follows:
ComponentComponent RequirementsRequirements
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Oxford Nanopore Technologies, the Wheel icon, GridION, Metrichor, MinION, MinKNOW, PromethION, SmidgION and VolTRAX are registered trademarks of Oxford Nanopore Technologies Limited in various
countries. © 2008 - 2021 Oxford Nanopore Technologies. All rights reserved. Registered Office: Oxford Science Park, Oxford OX4 4GA, UK | Registered No. 05386273 | Privacy Policy
1x RJ45 port IP address via either DHCP service OR statically assigned
TCP running on port 80 HTTP and port 443 HTTPS
Requires perimeter firewall permissions:
- To access AWS eu-west-1 IP ranges listed at https://ipranges.amazonaws.com/ip-ranges.json for telemetry feedback
and EPI2ME analysis
- To 178.79.175.200 and 96.126.99.215 for software updates
Connected to local storage infrastructure
1x power
supply
1x country-specific C13 cable included with device
- Maximum power draw 650 W
- Maximum current 6 A
- Supply voltage 100–240 VAC (50/60 Hz)
1x monitor Compatible with HDMI or DisplayPort connection (a DisplayPort to HDMI adapter is included in the GridION shipment)
1x keyboard Compatible with USB connection
1x mouse Compatible with USB connection
ComponentComponent RequirementsRequirements
Networking explanationsNetworking explanations
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
TelemetryTelemetry
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 EPI2ME platform is hosted within AWS and provides cloud-based analysis solutions for multiple applications. Use of this platform entails users uploading
sequence data in FASTQ format from the EPI2ME Agent, which is then processed through defined pipelines within the EPI2ME Portal. Downloads from
EPI2ME are either in Data+Telemetry or Telemetry form. Telemetry information is used to populate reports within the EPI2ME portal.
Software updatesSoftware updates
The IP address from which you receive software updates will depend upon your geographical location. Updates are performed through aptapt on the terminal,
therefore outbound-only access is required. Users are notified of the availability of software updates through the Nanopore Community, and full instructions for
updating are provided in each release note.
StorageStorage
File typesFile types
Nanopore sequencing data is stored in two file types, .fast5 and FASTQ. Basecalling summary information is stored in a
sequencing_summary.txt
file:
.fast5 is a customized file format based upon the .hdf5 file type, which is designed to contain all information needed for analysing nanopore sequencing
data, including raw signal data, and tracking it back to its source. As default, each .fast5 file will contain 4000 reads although this can be configured
when starting a run. The size of a .fast5 file size will depend on the number of reads contained and the length of DNA/RNA sequenced. See the table
below for estimates of storage space required for a typical sequencing run.
FASTQ is a universal text-based sequence storage format, generated when the nanopore signal data is basecalled and containing both the sequence
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Oxford Nanopore Technologies, the Wheel icon, GridION, Metrichor, MinION, MinKNOW, PromethION, SmidgION and VolTRAX are registered trademarks of Oxford Nanopore Technologies Limited in various
countries. © 2008 - 2021 Oxford Nanopore Technologies. All rights reserved. Registered Office: Oxford Science Park, Oxford OX4 4GA, UK | Registered No. 05386273 | Privacy Policy
of DNA/RNA and its quality scores. By default, the device saves up to 4000 sequences in one FASTQ file. The size of a FASTQ file will depend on the
number of reads contained and the length of DNA/RNA sequenced. See the table below for estimates of storage space required for a typical
sequencing run.
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.
Typically, 1 Gbase of sequence data takes up approximately 11 Gbytes of storage. This typically comprises of 90% .fast5 files, 9% FASTQ files and 1%
sequence summary file.
Example file sizes below are based on different throughputs from an individual flow cell, with a run saving both .fast5 and FASTQ files with a read N50 of 25
kb. The GridION can run up to five flow cells simultaneously.
Output (Gbases)Output (Gbases) .fast5 storage.fast5 storage
(Gbytes)(Gbytes)
FASTQ storageFASTQ storage
(Gbytes)(Gbytes)
.fast5 + FASTQ storage.fast5 + FASTQ storage
(Gbytes)(Gbytes)
1010 100 10 110
1515 150 15 165
3030 300 30 330
As an experiment progresses, .fast5 files are produced for all reads. If basecalling is chosen, these reads are utilised by the on-board software (more
information below) to generate sequence data which is then stored in FASTQ files.
Long-term storageLong-term storage
The GridION has sufficient SSD disk space for multiple runs to be carried out, storing both .fast5 and FASTQ data. 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.
The GridION runs on Ubuntu and is able to 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 .fast5 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 .fast5 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.
Included SoftwareIncluded Software
Oxford Nanopore Technologies build and provide numerous software types involved in acquisition, orchestration and analysis:
MinKNOWMinKNOW
MinKNOW carries out several core tasks:
Device control, including run parameter selection
Data acquisition
Real-time analysis and feedback
Data streaming
Basecalling (through integrated Guppy)
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
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Oxford Nanopore Technologies, the Wheel icon, GridION, Metrichor, MinION, MinKNOW, PromethION, SmidgION and VolTRAX are registered trademarks of Oxford Nanopore Technologies Limited in various
countries. © 2008 - 2021 Oxford Nanopore Technologies. All rights reserved. Registered Office: Oxford Science Park, Oxford OX4 4GA, UK | Registered No. 05386273 | Privacy Policy
.fast5 or FASTQ files.
GuppyGuppy
Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies' basecalling algorithms, and several bioinformatic post-processing
features. It is run from the command line, but has a low entry level for use. A selection of configuration files allow basecalling of DNA and RNA libraries, made
with Oxford Nanopore Technologies current sequencing kits, in a varied range of flow cells.
If rebasecalling off the GridION, it is possible to use an external GPU to basecall with Guppy, and this will dramatically increase basecalling speed over using
CPU. Guppy currently works with only NVIDIA GPUs, with the following specific models supported:
NVIDIA Volta GV100
NVIDIA Tesla V100
NVIDIA GTX1080Ti
NVIDIA Jetson TX2
It is possible to use other NVIDIA GPUs for basecalling, but support for those is limited.
EPI2MEEPI2ME
The EPI2ME platform is a cloud-based data analysis service offering a number of workflows for end-to-end analysis of nanopore data. The basecalled read
files from a sequencing run can be uploaded to the EPI2ME platform via another piece of software called the Desktop Agent. The user selects a workflow in
the Agent such as 16S alignment or Barcoding, and the Agent transfers the read files one by one into the cloud for real-time analysis. The analysis results are
generated and updated in real-time in the form of a report in the EPI2ME platform.
Frequently asked questionsFrequently asked questions
Can I use an uninterruptible power supply (UPS) with the GridION?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?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 rsyncrsync run hourly through crontabcrontab. For further details, please email support@nanoporetech.com
Change logChange log
DateDate VersionVersion Changes madeChanges made
9th July 2018 V1 Initial version
29th July 2019 V2 Updated information for GridION Mk1
29th April 2020 V3 Amended output file sizes after the introduction of file compression
14th September
2020
V4 Removed references to DisplayPort compatibility, as the GridION is now shipped with a DisplayPort to
HDMI adapter
12th November
2020
V5 Corrected DisplayPort and HDMI compatiblity
Page 5 of 5
GridION Mk1 IT requirements
Oxford Nanopore Technologies, the Wheel icon, GridION, Metrichor, MinION, MinKNOW, PromethION, SmidgION and VolTRAX are registered trademarks of Oxford Nanopore Technologies Limited in various
countries. © 2008 - 2021 Oxford Nanopore Technologies. All rights reserved. Registered Office: Oxford Science Park, Oxford OX4 4GA, UK | Registered No. 05386273 | Privacy Policy
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