# Tips and tricks for navigating the Linux Environment on the NextSeq 1000/2000

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:

1. Select **Applications** on the top left
2. Select **Internet**
3. Select **Chromium Web Browser**

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-27474d2514615714e09e17de62b00a57c4f249d6%2Fimage1.png?alt=media\&token=55dd0b09-b9b5-478f-96c9-6b55ce7d6264)

**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\
  ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-12019d2cb26a0f9b6869720251d47367739a8690%2Fimage2.png?alt=media)
* 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 ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-217ad592800a3af96079d66f3ee4e5c69f408fb6%2Fimage3.png?alt=media)
* If the illumina folder is not visible on the left, navigate to: Other Locations > Computer > usr > local > illumina\
  ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-bfbfc895e52795216bcefa29799956f1bee26d5b%2Fimage4.png?alt=media)

**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\
   ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-3b29d5613034c209ff221f0775c7507244582883%2Fimage5.png?alt=media)

**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…**\
   ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-d248c438b874a364e1a446ae9a16dcc7d973beb3%2Fimage6.png?alt=media)
3. In the next pop-up window, select **Create** to create a \*.tar.gz file on the desktop\
   ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-7f0db18c1848546d71479fad943febd44099d757%2Fimage7.png?alt=media)
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**\
   ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-97860afe7fbcb245160822cfefc1cf061c0d67f7%2Fimage8.png?alt=media)

**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\
  ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-4859d7a25a798dea44481bb515bba540a2ba0b63%2Fimage9.png?alt=media)
* teamviewerqs folder on the desktop\
  Double-click to open the folder and then select **teamviewer** to open the application\
  ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-948e9d6ea46ecfdb334ae935ffd5151a79b46b7c%2Fimage10.png?alt=media)
* 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**\
  ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-6b5250090b811f4cda3be5d5a789a037f9e96bcf%2Fimage11.png?alt=media)
* TeamViewer is listed under: Applications > Internet > TeamViewer\
  ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-d99b94e0c74bf97844ac80b9d050da3b0c5629dc%2Fimage12.png?alt=media)

**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**\
      ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-b9d5c2ce8dc312531568920c24ce196f91930f0f%2Fimage13.png?alt=media)
2. Enter in the command provided by Illumina Support and press
   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 ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-658bf131b7e2ece4ba3bdc29d3b5cd6346e92419%2Fimage14.png?alt=media)

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #3344), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000003344%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |