From portable to high-throughput benchtop devices, real-time nanopore sensing is a new generation of technology uncovering new biology across multiple sectors.
January 2025
- In "Computer requirements for MinKNOW", removed outdated information about firewall settings needed to run the MinION, and added a new section about security considerations.
12/31/2024
MKE_1013_v1_revDI_31Dec2024
English
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31st December 2024
- Formatting corrections in Section 21 *Save and load sequencing run settings* , subsection *Sequencing parameters using a JSON file*
- Amended description of __Control__ checkbox on kit selection page in *Starting a sequencing run with Flongle/MinION/GridION/PromethION*, step 3
12/18/2024
MKE_1013_v1_revDH_18Dec2024
English
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18th December 2024
- Broken anchor links fixed
12/11/2024
MKE_1013_v1_revDG_11Dec2024
English
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11th December 2024
- Added links to computer requirements for MinION Mk1C, PromethION 2 Solo and PromethION 2 Integrated.
- In "Starting a sequencing run", new information has been added for adaptive sampling settings: there is now an option to basecall on-target reads only and not basecall rejected reads.
- Updates to instructions for working with sample sheets in "Sample sheet upload" and "Save and load sample sheets"; order of these two sections switched
- Updates to "Downloading and installing MinKNOW" due to new combined installer for standalone MinKNOW for Windows and Linux
- Updated instructions for "Choose you analysis workflow options" in "Starting a sequencing run on PromethION 24 and 48" describing how to set up an EPI2ME wf-human-variation analysis workflow
- Replaced start page screenshots throughout to reflect new layout
- Added a note to "Choose your alignment options" in "Starting a sequencing run" sections for all devices describing validation of BED files upon upload
- Amended "Mac OS" to "macOS" throughout
11/22/2024
MKE_1013_v1_revDF_22Nov2024
English
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22nd November 2024
- Updates to snippet: Sequencing parameters using a JSON file.
- Addition of the MinION Mk1D device and corresponding links that include this device.
11/18/2024
MKE_1013_v1_revDE_11Apr2016
English
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18 Nov 2024
Updates to snippet: Sequencing parameters using a JSON file
22nd August 2024
- "Introduction to local basecalling": the basecaller speed benchmarking table has been corrected.
8/22/2024
MKE_1013_v1_revDE_11Apr2016
English
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22nd August 2024
- "Introduction to local basecalling": the basecaller speed benchmarking table has been corrected.
31 July 2024 - MinKNOW 24.06 updates
- In "Installing MinKNOW on Linux", instruction for installing MinKNOW on Ubuntu 18 have been removed.
- Updated images for run configuration in “Save sequencing run settings”.
- Included description and images of new FAQ “Help” feature implemented into the user menu, located in the “Troubleshooting your device” section of the document.
- Updated “Starting a sequencing run” section for all devices, including updated features and new images for UI.
- Added a “Starting a sequencing run” section for the PromethION P2i.
- Updated the “Post-run basecalling” section of the protocol, including updated features and new images for UI.
- Updated the “Post-run barcoding” section of the protocol, including updated features and new images for UI.
- Updated the “Post-run alignment” section of the protocol, including new images for UI.
- In "Introduction to local basecalling", basecalling keep-up benchmarks have been added.
16th April 2024
In "Installing MinKNOW on Linux", new instructions have been added for installing MinKNOW on Ubuntu 22.04. Also, the location of the Dorado basecaller log files has been added.
4th October 2023
- Added a new section "Introduction and quick start guides" which include a brief introduction to the MinKNOW software along with a quick start guide to set up our devices to sequence a library.
2023
5.7 MinKNOW release:
- In "Post-run basecalling", selecting the basecalling model has be updated and simplified.
- The "Run report" section has been updated with new screenshots of the run report, highlighting the new features of downloading a run report during a sequencing run. A barcoding table and graphs as well as an alignment table are now included in the run reports.
- The "Checks and monitoring" section now includes screenshots of the updated alignment hits graph with BED files.
29th June 2023
- Removed "Configuring a GPU version of Guppy with MinKNOW for MinION or PromethION 2 Solo on Windows" as the installer on the Community Downloads page is available.
21st June 2023
In "Configuring a GPU version of Guppy with MinKNOW for MinION or PromethION 2 Solo on Windows/Linux":
- For Windows, CUDA Toolkit 11.8 requirement has been added
- For Linux, the Troubleshooting section has been updated with clearer stepwise instructions
- An erroneous reference to guppyd-cpu has been removed
May 2023
- Throughout the document, screenshots have been updated to the most recent GUI version: software release 23.04.X
In "The Graphical User Interface (GUI)":
- Removed repeated screenshots from other devices.
- Added a new page: "Save sequencing run settings" detailing how to save sequencing parameters as a template and to join previously run experiments.
- In "Sample sheet upload", clarified which parameters in a JSON file to enable for enabling methylation calling and updated run until settings.
- Removed the "Host settings" page.
In "Host settings":
- Updated how to navigate to the host settings and the availability of settings on our devices.
- Updated "Data Management" how to use the "select all", "copy", "move", and "delete" options.
- In "Network settings and connection", added details for configuring static IP address.
In "Starting a sequencing run" for all devices:
- Removed how to log in to the software and now starts straight from opening start sequening run.
- Removed tips for saving settings and added location for finding how to use previously saved settings.
- Added how to find control sequencing parameters and a note to remind run time is reduced.
- Removed reference to sequencing speed as this option is removed from the new MinKNOW software version.
- Detailed how to use the updated "Run until" settings.
- Combined the "Analysis" section and user option snippets to clearly define how to alter settings.
- Updated the output tab format to explain how to alter settings.
- FAST5 output option is now labelled "(legacy)".
- Updated number of active pores at the beginning of a sequencing run tips.
- Updated how to stop a sequencing run prematurely.
In "Monitoring and troubleshooting your sequencing run":
- Updated the "Checks and monitoring", updated the experiment summary information.
In "Downloading and installing MinKNOW":
- Install name and Linux command for the standalone MinKNOW software have been updated.
15th May 2023
The sections "Configuring a GPU version of Guppy with MinKNOW for MinION or PromethION 2 Solo on Windows" and "Configuring a GPU version of Guppy with MinKNOW for MinION or PromethION 2 Solo on Linux" have been updated to remove installation instructions and add two new configuration use cases.
February 2023
- Updated information in "Connecting to device: Login and logout"and "starting a sequencing run" for how users log into MinKNOW software using their Community credentials which now requires the use of OKTA as user authentification.
- Updated screenshots of Connection manager and included information for adding remote devices in "Connecting to device: Connection manager" and "starting a sequencing run".
- Updated Filtering options to include the newly added POD5 output format for all devices in "Starting a sequencing run".
- Included new information for how to fail unaligned reads during sequencing set up for all devices in "Starting a sequencing run".
- Updated screenshot of pore activity and pore scan graphs with the improved order of categories in the legend in the "Monitoring and troubleshooting your sequencing run: Checks and monitoring".
- Updated the "Experiments page" of "The Graphical User Interface (GUI)" to include information on how to see previous experiments.
- Included information in "Starting a sequencing run" for all devices regarding the use of the reserved pore feature in the relevant 'Advanced user options' step.
- In the "Host settings: Troubleshooting', clearer information about the function of 'Clean up files' have been included.
- In 'Graphical User Interface (GUI): Sample sheet upload' kit name formatting information have been corrected
- In 'Monitoring and troubleshooting your sequencing run: Troubleshooting your run from pore activity plots', Low pore occupancy screenshot has been updated to a more accurate representation of low pore occupancy and updated recommendations.
7th December 2022
Minor updates and improvements to the protocol, including:
- The "Installing a GPU version of Guppy with MinKNOW" sections have been added back in to the protocol, as MinION and PromethION 2 devices may still require manual GPU configuration.
- Improved explanation of parameters to enter in sample sheet.
- Improvements in wording and typo corrections throughout the protocol.
1st November 2022
- "Installing MinKNOW on Linux" - new instructions have been added for installing MinKNOW for use with a GPU.
- "Starting a sequencing run" - the description of the "Trim barcodes or alter barcoding score" has been corrected to "Off by default".
- A new section has been added: "Starting a sequencing run on P2 Solo"
31st October 2022
- Updated screeshots in "Application settings" and updated information about changing languages on MinKNOW
- "Host settings" updated with additional information about Beta features
- "Starting a sequencing run with Flongle" has been updated with Kit 14 features
- "Starting a sequencing run" for all devices has been updated for new read splitting parameters
- The "Installing a GPU version of Guppy with MinKNOW for MinION on Linux/Windows" sections have been removed, as GPU-compatible installers are now available.
- "Installing MinKNOW on Windows/Linux" - installation instructions now include GPU installers, and new instructions have been added for setting GPU parameters for lower-memory graphics cards.
- "The Graphical User Interface (GUI)" - instructions for uploading CSV and JSON files in the "Sample sheet upload" have been corrected
17th October 2022
"Installing a GPU version of Guppy with MinKNOW for MinION on Linux" - the command in step 4 has been corrected, and all mentions of guppyd have been updated to guppyd-cpu.
16th September 2022
"Installing a GPU version of Guppy with MinKNOW for MinION on Linux/Windows" - for Linux, the commands in steps 5 and 6 have been updated. For Linux and Windows, the instructions for "Make sure the archive version of Guppy runs on your machine" have been updated.
12th September 2022
"Installing a GPU version of Guppy with MinKNOW for MinION on Linux/Windows" - more information has been added to "Setting GPU parameters for lower-memory graphics cards" on configuring GPUs for Guppy.
24th August 2022
Updated to reflect main updates for MinKNOW 22.08 release:
- 'Updating or re-installing MinKNOW': the 'MinKNOW updates for Windows and Mac OS X' has been updated to include information about update availability
- 'Starting a sequencing run' has been updated for all devices to include information about modified basecalling model for Kit 14, as well as Kit 14 sequencing speed and run report generation at the end of a run, including a new screenshot.
- 'Monitoring and troubleshooting your sequencing run': 'Checks and monitoring' has been updated regarding speed normalisation influence on the temperature graph, and a note has been added to the the translocation graph regarding sequencing speed selected for Kit 14. Additionally, the screenshots of flow cell health have been replaced with images for Flongle, MinION/GridION, and PromethION.
- 'Completing a MinKNOW run' has a 'Run report' section added to document the run report generated at the end of a sequencing run.
Other updates:
- In 'Flow cell check', the instruction for starting the flow cell check has been updated to say "When you see the flow cell type and flow cell IDs recognised, click 'Start' to begin."
- 'Troubleshooting your run from the pore activity plots' - screenshots of pore activity plots showing good and faulty libraries have been replaced with screenshots from the latest UI
4th July 2022
- Updated terminology used in the kit selection steps of the 'Starting a sequencing run' section
- Updated the image used to illustrate accessing the tutorials in the GUI
26th May 2022
- Updated 'Starting a sequencing run' to include how to join an existing sequencing run, new information on support for the super-accurate basecaller - plant using the maize model
- Updated 'Homepage' in 'The Graphical User Interface (GUI)' with updated screenshot of the GUI with the 'Applications settings' with updated instructions to find application settings
- Updated 'Starting a sequencing run' to include new information on the beta barcode balancing and new adaptive sampling support for MinION Mk1C and PromethION. Also updated screenshots throughout this section for the new basecaller page
- Added information in the 'Network settings and connection' section about how to configure the wifi hotspot to use a different channel
- Updated the 'Sample sheet upload' section to include updated information when uploading a JSON file, including new rules for uploading the sample sheet
30th March 2022
- In "Installing a GPU version of Guppy with MinKNOW for MinION on Linux/Windows", the "Setting GPU parameters for lower-memory graphics cards" section has been updated to include a note to restart the guppyd/Windows service after the settings have been updated. Also, the Troubeshooting instructions have been condensed into one box for clarity.
24th March 2022
- In "Installing MinKNOW on Linux", removed instructions for installing MinKNOW on Ubuntu 16.04 (Xenial)
- Updated image of the software tab in the 'Host settings' 'Overview' sections
23rd March 2022
Updates include:
- Added information about the system overview included in the new MinKNOW release in the Graphical user interface (GUI) and Host settings sections.
- Added a new graph illustrating Kit 12 translocation in the checks and monitoring section
- Updated image for output settings in 'Starting a sequencing run'
- Added information on how to set up short fragment mode in 'Starting a sequencing run'
- Updated how to export the run report in 'Starting a sequencing run'
- Updated references from Duty Time plot to 'Pore Activity plot' and 'Mux scan' to 'Pore scan'.
9 February 2022
- In "Downloading and installing MinKNOW", the installation instructions for Mac OS X have been updated. Also, manually setting the directory where read files will be saved is now an optional step.
2nd February 2022
- In "Installing a GPU version of Guppy with MinKNOW for MinION on Linux", a new step has been added: "Rename the existing override.conf file so that it does not override our new settings".
- In "Installing a GPU version of Guppy with MinKNOW for MinION on Windows", the names of some of the parameters in Step 5 have been updated.
26st November 2021
- Updated 'Starting a sequencing run on GridION' with new screenshots for choosing basecalling, barcoding and alignment options. Also updated information once sequencing is completed and how to show previous runs older than 7 days.
21st November 2021
- Added installation instructions for Ubuntu 20 in 'Installing MinKNOW on Linux'
- Clarified when 'Get update' is clicked when connected to a MinION Mk1B, the Software Downloads page is opened rather than the update being automatically updated. We have also added information that a changelog will be included in the installer dialogue on the MinKNOW UI. This is in section 'MinKNOW updates for Windowns and Mac OS X'.
- Added a new section in 'Connecting to device' titled 'Device Security Settings' to explain how to alter device security settings and which accounts can connect to a device.
- Updated the 'Hardware check' section to include information in the "important" snippet, explaining how to check the Flongle flow cell adapter. This instruction is reiterated in the relevant Flongle section of the "action" steps.
- Added information in the 'Host settings' section to use the power button for the MinION Mk1C to shutdown or reboot the device.
- Updated the "tip" user options with an updated screenshot of the barcoding options in the 'Starting a sequencing run' for all devices.
- Added how to find experiments older than the default seven days in the final "action" step of the 'Starting a sequencing run' for all devices.
- Updated the read length histogram image and the read length historgram definitions with the added conditions in the 'Monitoring and troubleshooting your sequencing run' section.
- Added a new snippet in the 'Monitoring and troubleshooting your sequencing run' section with information explaining the Mux scan graph.
- Updated the post-run analysis screenshot in the 'Post-run analysis' section.
- Screenshot of the 'Output' tab in the 'Post-run basecalling' section to show the 'Output .fast5 files' toggle is no longer on by default.
27th October 2021
- Added a new section, "Installing a GPU version of Guppy with MinKNOW for MinION on Windows"
- Added troubleshooting instructions in "Installing a GPU version of Guppy with MinKNOW for MinION on Linux"
27th September 2021
- "Mount network drive": more detail has been added about when an SMB vs NFS share can be used.
- "Network settings and connection": in the section about activating the MinION Mk1C hotspot, the image of the Mk1C serial label has been updated
17th September 2021
- In "Starting a sequencing run", information about the available basecalling models has been updated to reflect the current selection: Fast, HAC, SUP, 5mC, or no basecalling. The basecalling accuracy numbers have also been updated.
- In "Checks and monitoring", the section on pore occupancy has been updated with the correct definition of Adapter: "the pore is sequencing the unligated sequencing adapter only. Reads will initially be classified as adapter until the DNA/RNA strand starts translocating through the pore and MinKNOW™ is able to reclassify the read".
9th September 2021
In "Downloading and installing MinKNOW", some details in the "Installing a GPU version of Guppy with MinKNOW for MinION" step have changed:
- GPU basecalling on Windows is now supported
- The "Modify MinKNOW's application configuration to enable GPU basecalling and set the appropriate settings." instruction has been removed
- Instead, instructions for editing and running the guppyd service have been added
16 June 2021
- All screenshots have been updated to the updated MinKNOW 4.3 GUI.
- Updated login image in the 'Connecting to device: login' section and added information to logout of the software. Login image also updated in section 'Starting a sequencing run' for all devices.
- Added information in 'Connecting to device: login' to include instructions for logging out of the MinKNOW software
- Updated 'The Graphical User Interface (GUI): Homepage', 'Homepage overview' snippet to new screenshot of the GUI and updated options.
- Added image to highlight the harware check option in 'The Graphical User Interface (GUI): Hardware check'
- Updated 'The Graphical User Interface (GUI): Experiments page' with updated information fort the experiments page snippet
- How to pause a sequencing run and triggering a mux scan updated in 'The Graphical User Interface (GUI): Experiments page'
- Added new sections in 'The Graphical User Interface (GUI)': 'Sample sheet upload' to explain how to upload a sample sheet before a sequencing run; and 'MiniMap index generation' to explain how to generate a minimap index prior to setting up a sequencing run with live alignment
- 'The Graphical User Interface (GUI): Application settings' updated to include how to change language between English and Mandarin
- Renamed 'Admin interface' to 'Host settings'. All reference to 'admin interface' have now been updated to 'host settings'
- Updated 'Features of the Host settings' in 'Host settings: Overview' with new screenshot and updated features of the Help section
- 'Host settings: Data management' updated as 'share on Samba network' toggle has moved from the file manager to device settings.
- In 'Host settings: Data management', the file manager options now only appear on page when the select toggle is active
- Information regarding the 'Clean up' option on 'Host settings: Export logs' added
- In 'Starting a sequencing run' for all devices, 'Saved and default settings' snippet has been updated to reflect name change to 'Load settings from template'
- The 'Skip to end' snippet in 'Starting a sequencing run' for all devices has been updated to name change: 'Skip to final review'
- 'Save settings' option has changed name to 'Save settings as template' on the review page
- Generating an export PDF at the end of a sequencing run in 'Starting a sequencing run' for all devices has been updated as the 'Export PDF' option is now available in the options bar of the experiments page
- In 'Starting a sequencing run on GridION', the optional action snippet highlighting how to upload a sample sheet has been shortened with the addition of a link to the 'Sample sheet upload' section within the protocol with more detailed instructions
- In 'Monitoring and troubleshooting your sequencing run: Refuelling your flow cell', instructions for pausing and starting a new mux scan on a flow cell have been updated
- In 'Monitoring and troubleshooting your sequencing run: Checks and monitoring', graphs have been updated for: read length histogram, cumulative output, cumulative output of multiple flow cells, temperature and bias voltage graph, translocation speed and Qscore graphs, barcodes read counts, alignment hits, alignment and barcode heatmap
- In 'Monitoring and troubleshooting your sequencing run: Checks and monitoring', updated split read end reasons on the read length histogram graph screenshot.
- How to stop a sequencing run screenshot has been updated in 'Completing a MinKNOW run: Completion of a sequencing protocol script'
- in 'Installing GPU version of Guppy with MinKNOW for MinION', a disclaimer was added: "Note that the version of Guppy must match the version packaged within MinKNOW to prevent errors. The exact version to use can be obtained from the output of Step 1 or from the MinKNOW release notes".
7th April 2021
- In the "Downloading and installing MinKNOW" section, "Installing GPU version of Guppy with MinKNOW for MinION", added an instruction to identify the version of the Guppy basecall server that MinKNOW is using. Also, the command for set guppy.client_executable has been updated to reflect changes released in Guppy version 4.5.2
10th March 2021
- In the "Starting a sequencing run on the MinION Mk1C" section, instructions have been added to enable adaptive sampling for the initial MinION Mk1C release.
16th February 2021
- In the "Monitoring and troubleshooting your sequencing run" section, "Troubleshooting your run from the Duty Time plots" step, updated the link to the the Flow Cell Wash Kit protocol from EXP-WSH003 to EXP-WSH004
- In the "Starting a sequencing run" section, "Starting a sequencing run on PromethION" step, added a description of the Modified basecalling model for 6mA dam/5mC dcm and CpG
20th December 2019
Updates for MinKNOW release v19.12.4 for PromethION, featuring:
- Post-run basecalling updates - demultiplexing and folder creation enabled
- Updated PDF report
- Barcode trimming and graph of barcodes in the GUI
- New configurable compression options (VBZ for .fast5 and gzip for FASTQ)
- Updates to file names and locations to consolidate data per run
- GUI updates - disk write speed graph, Trigger MUX Scan button and updates to read length histogram
- Protocols updates - Improved MUX scan voltage during runs and MinKNOW allows time for strands to finish prior to starting MUX scan
- Script configuration is reported in MinKNOW about box
- Channel scans enabled for Flongle
- Sequencing Summary updated to include end_reason
- Rename of positions in file paths and on the GUI reflect the actual names on the box
- Device identification - P24- and P48-specific GUI
- Support for upcoming kits
- Bug fix for ModBaseProbs naming when generated in MinKNOW
5th December 2019
Updates for MinKNOW release v19.12.2 for MinION and GridION, featuring:
- Post-run basecalling updates - demultiplexing and folder creation enabled
- Updated PDF report
- Barcode trimming and graph of barcodes in the GUI
- New configurable compression options (VBZ for .fast5 and gzip for FASTQ)
- Updates to file names and locations to consolidate data per run
- GUI updates - disk write speed graph, Trigger MUX Scan button and updates to read length histogram
- Protocols updates - Improved MUX scan voltage during runs and MinKNOW allows time for strands to finish prior to starting MUX scan
- Script configuration is reported in MinKNOW about box
- Channel scans enabled for Flongle
- Sequencing Summary updated to include end_reason
- Rename of positions in file paths and on the GUI reflect the actual names on the box - X1, X2, X3, X4 and X5
- Support for upcoming kits
- Bug fix for ModBaseProbs naming when generated in MinKNOW
27th November 2019
- New instructions for starting a sequencing run on the MinION Mk 1C
- Explanation of the MinION Mk 1C graphical user interface and experiment summary screen
30th October 2019
- Updated information on configuring the number of .fast5 files per folder/FASTQ reads per file during experiment set-up
- Added information about duty time/cumulative output CSV files produced by MinKNOW
8th October 2019
The MinKNOW protocol has had content introduced to reflect the MinKNOW 19.10 release.
These changes include:
- Demultiplexing in MinKNOW as an option under __Kit selection__
- Modified basecalling model in __Basecalling model type__
- Post-run basecalling as an option in __Post-run analysis__
- Warning message about data writing speed, if it is too slow to keep up, in the __Output__ section
8th October 2019
The MinKNOW protocol has had content introduced to reflect the MinKNOW 19.10 release.
These changes include:
- Demultiplexing in MinKNOW as an option under __Kit selection__
- Modified basecalling model in __Basecalling model type__
- Post-run basecalling as an option in __Post-run analysis__
- Warning message about data writing speed, if it is too slow to keep up, in the __Output__ section
8th October 2019
The MinKNOW protocol has had content introduced to reflect the MinKNOW 19.10 release.
These changes include:
- Demultiplexing in MinKNOW as an option under __Kit selection__
- Modified basecalling model in __Basecalling model type__
- Post-run basecalling as an option in __Post-run analysis__
- Warning message about data writing speed, if it is too slow to keep up, in the __Output__ section
29 July 2019 - Rev AR
'Refuelling your sequencing experiment' section added into 'Monitoring and troubleshooting your sequencing run'. There are links out of the 'starting a sequencing run [of relevant flow cell]' sections to the Refuelling section.
10 July 2019
Added warning: "Please note that in the current version of MinKNOW, stopping your experiment and stopping basecalling through the GUI when ONLY FASTQ output is selected leads to queued reads being discarded. We are working on a fix."
09 July 2019
Added instructions and images for MinKNOW on Flongle, GridION and PromethION. Removed obsolete instructions for old versions of the software.
Updated with new information for MinKNOW release v19.06:
- Compression of queued reads
- Pause functionality
- UI improvements including:
- Flow cell health at platform QC
- Flow cell status on landing page
- R10 flow cell running scripts
- New Fast Models for RNA and DNA
- PDF report and CSV files for Duty time and Cumulative output are now found in same location as actual reads and fastQ files
- Flongle hardware check for confirming Flongle adapter functions correctly