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 bulletin 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:

1. Select Applications on the top left
2. Select Internet
3. 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:

• Use the Files navigation icon on the desktop of the instrument. Double-click the icon to access the illumina folder
  
• If there is no Files navigation icon on the desktop:
  1. Select Applications on the top left
  2. Select Favorites
  3. Select Files
  4. 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
  

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:

1. In the desired folder in the file navigation window, select the three lines on the top, right side
2. Select the bookmark icon in the middle
3. After selecting the bookmark icon, the new folder appears as a favorite on the left side
   

Collecting files to send for review

Similar to Windows, collect intended files in a new folder on the desktop:

1. Create a folder and copy and paste files/other folders into it
2. After files have been added to the folder, right-click on the folder and select Compress…
   
3. In the next pop-up window, select Create to create a *.tar.gz file on the desktop
   
4. 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:

1. Select Applications on the top left
2. Select Illumina
3. Select NextSeq 1000/2000 Control Software
   

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: 

• 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
  

How to Run a Command in Terminal

1. Launch the terminal:
   1. Select Applications in the top left
   2. Select System Tools
   3. Select Terminal
      
2. Enter in the command provided by Illumina Support and press <ENTER>
   1. 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