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Options to access your MinIT
There are several options to connect to your MinIT. These are:
- Default Folder browser for Linux - e.g. smb://mt-100007
- Connection Manager on the MinKNOW software
Advanced users
- Secure Shell access -
ssh minit@mt-100007
in a terminal
Please ensure you have downloaded the 'MinIT Software' for your operating system from the Software Downloads page.
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To access the MinIT, you can use the Linux File Browser and enter the server address.
To access your MinIT, open the File Browser (this can be found using the Search tool). Select Connect to server on the bottom of the list in the left panel. You will need to enter:
`smb://mt-100007`
in the window shown below.
Clicking Enter in this panel, will enable access to the MinIT's data folder.
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To access the MinIT on the Wi-Fi network, enter the MinIT username and password in the appropriate tabs as shown in the window below.
Username: minit
Password: minitNote: The password and username are case-sensitive. The login credentials stated here are also required to connect to a wired network.
Below shows the window that is displayed to access the MinIT network through the wireless or wired connections. The network contains the data folder.
To access the MinIT on the Wi-Fi network, enter the below username and password in the appropriate tabs as shown in the below window.
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This will open a window containing a 'data' folder.
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Within the 'data' folder, a MinKNOW icon with the title 'MinKNOW' can be found – double-click on this to open the MinKNOW interface.
The icon named 'MinKNOW.url' will guide the user to MinKNOW, the sequencing software. -
OR, you can access the device through the MinKNOW GUI by selecting the desktop icon.
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We recommend users to log into the MinKNOW software using their Community credentials.
If you experience login issues, please contact support via email (support@nanoporetech.com) or via LiveChat in the Nanopore Community and use Continue as guest for temporary use.
To login, you must be connected to the internet.
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Select 'Add Host' in the Connection Manager to open a new window.
Enter the MinIT host ID or IP address in the Add Host window to connect to the device.
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The MinION Mk 1B to be used to run a sequencing experiment MUST be plugged into the lower of the two USB ports (i.e. USB 2.0) with the MinIT in the orientation shown below.
The USB 2.0 port. The USB 2.0 port is the lower of the two USB ports (power right, ethernet left). The MinION Mk 1B should be plugged into this port to function, providing faster data transfer through the (upper) USB 3.0 for SSD storage.
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Options
Once the MinION Mk 1B is plugged into the USB 2.0 port in the MinIT, there are four options:
1. Hardware check
2. Flow cell check
3. Starting a sequencing run
4. Post-run basecallingThese are detailed below:
1. Hardware check
The Configuration Test Cell (CTC) is used for a hardware check that verifies the connections and that the devices are correctly functioning. A number of CTCs are provided with all the sequencing platforms sold by Oxford Nanopore Technologies. The user will also be instructed to check the hardware in the Quick Start Guide that comes with the MinIT.
You can find instructions for how to run a hardware check in the MinION Mk1B installation and configuration protocol.
2. Flow Cell Check
A flow cell has a warranty for a minimum number of pores, where the flow cell can be replaced if the flow cell does not meet this. The Flow Cell Check will quantify the number of functional pores and this check should be performed before the user starts the sequencing experiment.
Instructions on how to run a flow cell check can be found in the Flow Cell Check protocol.
3. Starting a sequencing run
An option exists where the user may have performed the Flow Cell Check and wants to run a sequencing experiment.
The flow cell should remain in the MinION Mk 1B, once the Platform QC has been completed, if the user intends to run a sequencing experiment shortly afterwards. The flow cell should be primed, the library loaded, and the experiment initiated with the flow cell in the MinION Mk 1B, as described in the Oxford Nanopore Technology protocols.
Instructions on how to start a sequencing experiment can be found in the 'Starting a sequencing run' section of the MinKNOW protocol.
4. Post-run basecalling
The MinIT can be used to re-basecall data generated from a nanopore experiment. The input is .fast5 files, containing raw data. The output is in a FASTQ format, containing the basecalled sequence with an associated quality score. Please use the MinKNOW protocol and follow the instructions in Post-run analysis, Post-run basecalling to re-basecall your .fast5 files.
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For details on how to co-ordinate and interpret your experiment in MinKNOW, whilst the MinION Mk 1B is sequencing, please refer to the link below:
The MinKNOW protocol describes how to install, run and interpret MinKNOW parameters during a sequencing experiment. The protocol can be found in the MinKNOW protocol
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The MinKNOW Sequencing Overview page will show your MinION Mk 1B and flow cell (below), indicating the status of your sequencing experiment.
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The output tab of setting up a sequencing run can be configured to set up your experiment.
To reach this page, select 'Start Sequencing' and navigate to 5. Output tab.