First Time Setup

The MiSeq i100 Plus Control Software guides you though the first time setup. The following sections summarize the configuration settings to be configured during initial setup.

Do not disturb the instrument if the spinning wait cursor is displayed. Disruption of the process can result in an unrecoverable critical system error.

Administrator Account

You can only create one administrator account during the first time setup. After it is set up, you can create additional administrator accounts. For more information, refer to Add Users.

• User name
• Password

Instrument Nickname

• [Optional] Instrument nickname

If you enter an instrument nickname, it displays at the bottom of the screen in the MiSeq i100 Plus Control Software.

Network Connection

Configuring the network connection during the first time setup procedure is optional, but recommended. If you do not configure the network, you must configure a USB or external storage. You cannot use Illumina Proactive, BaseSpace Sequence Hub, or any other cloud services until the network has been set up.

To use a static IP address, manually enter the IP address, or use Dynamic Host Configuration Protocol (DHCP) to automate the assignment of the IP address.

• Automatically assign IP address (DHCP)
• Manually enter IP address
– IP Address
– Netmask
– Gateway

If you are inputting the DNS servers manually, you can include multiple servers by separating them with commas. If the MiSeq i100 Plus is not on the domain, you can search for the domain to get name resolution.

• Automatically assign DNS server IP address
• Manually enter DNS server IP address optional
– DNS server(s) IP address
• Search domain optional

If a proxy server is enabled, an option to enter a user name and password displays for an authenticated proxy.

• [Optional] Enable proxy
– Server address
– [Optional] Port 
– Requires user name and password
• User name
• Password
• Time zone
• NTP Address optional

If you must access the MiSeq i100 Plus remotely, you must enable ports 80 and 443.

• Enable network ports 80 and 443 for remote access

Illumina Proactive

Illumina Proactive is selected by default.

• Send instrument performance data to Illumina. No sequencing data are sent.

System Checks

After the required configurations are in place, system checks are initiated to ensure the proper functioning of all the MiSeq i100 Plus components. The system checks include testing the flow cell door, internal cooling fan, and reagent loading mechanisms. Do not disturb the instrument as it undergoes the system checks. The system checks use the reusable wet and dry test cartridges, which are included with the MiSeq i100 Plus.

Load the reusable test cartridges as follows.

1. Select Next to extend the dry tray.
2. Load the dry test cartridge after the dry tray extends.
3. Select Next to retract the dry tray and extend the wet tray.
4. Load the wet test cartridge after the wet tray extends.
5. Press Next to retract the wet tray and start the system checks.

Do not adjust the trays manually. Doing so can lead to an unrecoverable critical system error.

If the system checks identify any failures, the system checks continue until all the components have been checked. A comprehensive list of the failed components is recorded in the log files. Contact Illumina Technical Support to share the log files and address any issues through troubleshooting.

After the system checks have completed, unload the reusable wet test cartridge and reusable dry test cartridge by selecting Eject Consumables from the Start screen. Store the cartridges at the ambient temperature for future use.

External Storage

Network storage - SMB

1. Enter the following information:
• Server location
• Domain optional
• User name
• Password

Encryption

• Require encryption during file transfer.
• Do not require encryption during file transfer.
2. Select Test configuration to test the network storage connection.
3. After the test completes, select Save.
4. Proceed to Specify default folder.

Network storage - NFS Storage

NFS storage does not require a user name or password, but the fields are present in the MiSeq i100 Plus Control Software. You can enter any values to proceed.

1. Enter the following information:
• Server location
• Domain optional
• User name
• Password
2. Select Test configuration to test the network storage connection.
3. After the test completes, select Save.
4. Proceed to Specify default folder.

USB Storage

Adding a USB drive for external storage is only recommended when MiSeq i100 Plus is not connected to a network. A USB drive can also be used to import Sample Sheets and resource files.

The USB drive must be configured as follows.

• Formatted to exFAT or NTFS.
• Contain a folder to be used as the output folder. The folder name cannot have a space.

The folder cannot be created in the MiSeq i100 Plus Control Software, it must be created before adding the USB to the instrument.

• Connected to the USB 3.1 port. Refer to Peripheral Connections.
1. Select Add USB

If the USB is encrypted, then enter the password. Do not enter a password if the USB is not encrypted.

2. Select Add.
3. Select Save.
4. Proceed to Specify default folder.

Specify default folder

After a local network storage has been added, the MiSeq i100 Plus Control Software will take you to the Start screen. A default folder must be set up before you can start to a sequencing run. Use the following steps to set the default folder.

1. Select the menu icon in the upper-left corner.
2. Select Settings, and then select External storage.
3. Select Add folder.
4. Select a server location from the drop-down list, and then select the volume.
5. Select the desired default output folder from Available folders.
6. [Optional] Enter a folder nickname.
7. Select Save.

If you are subscribed to Professional BaseSpace Sequence Hub (BSSH), the private domain name is required.

• Hosting location
• [Optional] Private domain name