Tips and tricks for navigating the Linux Environment on the NextSeq 1000/2000
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The NextSeq 1000/2000 is the newest Illumina sequencing system and was launched in the first half of 2020. The NextSeq 1000/2000 runs in the Linux environment instead of Windows, which is the operating system used by all other Illumina sequencing systems. Many users may not be as familiar with navigating Linux as they are with Windows. This article includes steps for simple functions on the NextSeq 1000/2000 to help users feel comfortable navigating Linux.
General instructions for shutting instruments down for an extended period of time
Finding a Web Browser
With the control software minimized:
Select Applications on the top left
Select Internet
Select Chromium Web Browser
File Navigation
Most files that are important for Illumina support are found at the following location: /usr/local/illumina/
There are several ways to navigate to the illumina folder:
If there is no Files navigation icon on the desktop:
Select Applications on the top left
Select Favorites
Select Files
Adding a folder location to favorites
Add a file location to the favorites section on the left side of the file navigation window to make it easier to navigate to this location in the future:
In the desired folder in the file navigation window, select the three lines on the top, right side
Select the bookmark icon in the middle
Collecting files to send for review
Similar to Windows, collect intended files in a new folder on the desktop:
Create a folder and copy and paste files/other folders into it
After the folder has been compressed into a \*.tar.gz file, it can be sent back to Illumina Support for further review
How to Launch the Control Software
Confirm that the control software is not minimized. If it is minimized, you will see it on the bottom left of the screen. To maximize, select the control software.
If the control software is not already open:
Select Applications on the top left
Select Illumina
How to Find TeamViewer
TeamViewer is the desktop share application that allows Illumina Support personnel to see remotely and share the NextSeq 1000/2000 computer.
There are several ways to access the TeamViewer application:
How to Run a Command in Terminal
Launch the terminal:
Select Applications in the top left
Select System Tools
Enter in the command provided by Illumina Support and press
Use the Files navigation icon on the desktop of the instrument. Double-click the icon to access the illumina folder
After the file navigation window pops up, the illumina folder may already be visible as a favorite or recent on the left-hand side
If the illumina folder is not visible on the left, navigate to: Other Locations > Computer > usr > local > illumina
After selecting the bookmark icon, the new folder appears as a favorite on the left side
After files have been added to the folder, right-click on the folder and select Compress…
In the next pop-up window, select Create to create a \*.tar.gz file on the desktop
Select NextSeq 1000/2000 Control Software
TeamViewer Icon on the desktop Double-click the icon to activate the application
teamviewerqs folder on the desktop Double-click to open the folder and then select teamviewer to open the application
teamviewerqs folder in downloads. Navigate to the downloads folder by opening a file navigation window (Applications > Favorites > Files) and find Downloads on the left-hand side. Select the teamviewerqs folder and select Teamviewer
TeamViewer is listed under: Applications > Internet > TeamViewer
Select Terminal
If the command includes the term sudo at the beginning of it, the ilmnadmin password is needed to perform the command. If so, after the command is entered a prompt appears, requesting the ilmnadmin password Note: The ilmnadmin password should be known by someone on site and is changed from the default password Illumina provides
For any feedback or questions regarding this article (Illumina Knowledge Article #3344), contact Illumina Technical Support .
