Illumina NextSeq 1000 and 2000 Site Prep Guide

Introduction

This guide provides specifications and guidelines for preparing your site for installation and operation of the NextSeq 1000/2000™ Sequencing System, including:

• Laboratory space requirements
• Electrical requirements
• Environmental constraints
• Computing requirements
• User-supplied consumables and equipment

Safety Considerations

Refer to the NextSeq 1000 and NextSeq 2000 Sequencing Systems Safety and Compliance Guide (document # 1000000111928) for important safety information.

Additional Resources

The Illumina website provides additional system resources, including software, training, compatible products, and documentation. Always check support pages for the latest versions.

Delivery and Installation

An authorized service provider delivers the system, uncrates components, and places the instrument on the lab bench. Ensure the lab space and bench are ready before delivery.

Caution: Only authorized personnel can uncrate, install, or move the instrument. Mishandling can affect alignment or damage components.

An Illumina representative installs and prepares the instrument. When connecting to a data management system or remote network location, ensure the data storage path is selected before installation. The representative can test the data transfer process during installation.

Access to instrument USB ports is required for installation, maintenance, and service.

Caution: After installation, do not relocate the instrument. Improper relocation can affect optical alignment and compromise data integrity. Contact Illumina if relocation is necessary.

Crated Dimensions and Contents

The NextSeq 1000 and NextSeq 2000 Sequencing System is shipped in one crate. Use the following dimensions to determine the minimum door width required:

The crate includes the instrument and the following components:

• Power cord (8 ft)
• Accessories kit (keyboard and mouse)

Laboratory Requirements

This section provides specifications and requirements for setting up your lab space. For more information, see Environmental Considerations.

Instrument Dimensions

A diagram shows the NextSeq 1000/2000 instrument.

Placement Requirements

Position the instrument to allow proper ventilation, access to power outlets, and access for servicing. Ensure personnel can quickly disconnect the power cord. Multiple instruments placed back-to-back must be offset at least 61 cm (24 in) on each side.

Clearance Requirements:

• Sides: Allow at least 50.8 cm (20 in) on each side.
• Rear: Allow at least 11.4 cm (4.5 in) behind the instrument.
• Top: Allow at least 61 cm (24 in) above the instrument.

Caution: Improper relocation can affect optical alignment and compromise data integrity. Contact Illumina if relocation is necessary.

Lab Bench Guidelines

Place the instrument on a sturdy lab bench away from vibration sources. The instrument should be isolated on a moveable bench. Measurements do not include the 5–10 cm required for cable management.

For North American customers, Illumina recommends the Bench-Tek Solutions lab bench (www.bench-tek.com), part #BT40CR-3048BS-PS.

Vibration Guidelines

Keep lab floor vibration at or below the VC-A standard of 50 µm/s for 1/3 octave band frequencies of 8–80 Hz. Do not exceed the ISO Operating Room standard of 100 µm/s for 1/3 octave band frequencies of 8–80 Hz.

To minimize vibrations during sequencing runs:

• Place the instrument on a sturdy lab bench.
• Do not place keyboards, used consumables, or other objects on top of the instrument.
• Do not install the instrument near sources of vibration exceeding the ISO Operating Room standard (e.g., motors, pumps, shake testers, heavy air flows, HVAC fans, construction/repair work, high foot traffic areas).
• Use only the touch screen, keyboard, and mouse to interact with the instrument. Do not directly impact instrument surfaces during operation.

Lab Setup for PCR Procedures

Some library prep methods require the polymerase chain reaction (PCR) process. Establish dedicated areas and lab procedures to prevent PCR product contamination.

Pre-PCR and Post-PCR Areas

Use the following guidelines to avoid cross-contamination:

• Establish a dedicated pre-PCR area for pre-PCR processes.
• Establish a dedicated post-PCR area for processing PCR products.
• Do not use the same sink for washing pre-PCR and post-PCR materials.
• Do not use the same water purification system for both areas.
• Store pre-PCR supplies in the pre-PCR area and transfer them to the post-PCR area as needed.

Dedicate Equipment and Supplies

• Do not share equipment and supplies between pre-PCR and post-PCR processes.
• Establish dedicated storage areas for consumables in each area.

Required Storage for Sequencing Consumables

Table 1 Kit Components

*Shipped at room temperature

Electrical Requirements

Power Specifications

Table 2 Instrument Power Specifications

Table 3 Server Power Specifications

Receptacles

Your facility must be wired with the following equipment:

• For 100-120 Volts AC: A 15 amp grounded, dedicated line with proper voltage and electrical ground is required. (North America and Japan—Receptacle: NEMA 5-15)
• For 220-240 Volts AC: A 10 amp grounded line with proper voltage and electrical ground is required. If voltage fluctuates more than 10%, a power line regulator is required.

Protective Earth

The instrument has a connection to protective earth through the enclosure. The safety ground on the power cord returns protective earth to a safe reference. Ensure the protective earth connection on the power cord is in good working condition.

Power Cords

The instrument is equipped with an international standard IEC 60320 C14 receptacle and ships with a region-specific power cord. Hazardous voltages are removed from the instrument only when the power cord is disconnected from the AC power source.

Caution: Never use an extension cord to connect the instrument to a power supply.

Fuses

The instrument contains no user-replaceable fuses.

Uninterruptible Power Supply

A user-supplied uninterruptible power supply (UPS) is highly recommended. Illumina is not responsible for runs affected by interrupted power.

The following table lists region-specific UPS recommendations:

For equivalent UPS options complying with local standards, consult Interpower Corporation (www.interpower.com).

Environmental Considerations

Heat Output

Noise Output

A measurement of ≤ 70 dB is within the level of a normal conversation at a distance of approximately 1 meter (3.3 feet).

Network Considerations

The NextSeq 1000 and NextSeq 2000 Sequencing System is designed for network use, whether connected to BaseSpace Sequence Hub or in manual run mode. The control computer runs CentOS with SELinux enabled. Encryption is not supported.

Manual mode requires a network connection to transfer run data to a network storage location. Do not save run data to the local hard drive; it is intended for temporary storage.

An internet connection is required for:

• Connecting to Illumina BaseSpace Sequence Hub.
• Uploading instrument performance data for Illumina Proactive Support (see Illumina Proactive Technical Note, document # 1000000052503).
• [Optional] Remote assistance from Illumina Technical Support.

Network Connections

Recommendations for installing and configuring a network connection:

• Use a dedicated 1 gigabit connection between the instrument and your local data management system, directly or through a managed network switch.
• Required bandwidth:
• 200 Mb/s/instrument intranet bandwidth for local storage.
• 5 Mb/s/instrument minimum internet bandwidth for downloading NextSeq 1000/2000 Control Software and DRAGEN Workflows (~15 GB). Download times out after 6 hours. 35 Mb/s/instrument internet bandwidth is required to download within 1 hour.
• 10 Mb/s/instrument internet bandwidth for BaseSpace Sequence Hub cloud storage (including Illumina Proactive Support).
• 5 Mb/s/system internet bandwidth for run monitoring or Illumina Proactive Support only.
• Switches must be managed.
• Intranet and local network equipment (e.g., switches) must have a minimum 1 gigabit per second rating.
• Calculate the total capacity of the workload on each network switch, considering connected instruments and ancillary equipment.
• If possible, isolate sequencing traffic from other network traffic.
• Cables must be CAT 5e or better; CAT 6 or better is recommended.
• Ensure required cables are available before starting installation.

Network Support

Illumina does not install or provide technical support for network connections. Review network architecture for potential compatibility risks.

• Potential IP address conflicts: The system assigns random internal IP addresses within the range of 169.254.0.0/16, which can cause system failure if conflicts occur.
• IP assignment: The system supports DHCP or Static IP assignment.

Control Computer Connections

A diagram illustrates the network connections for the control computer, including host network, switch, camera, and hardware controllers.

The following tables describe network ports and domains of the control computer.

Internal Connections

Outbound Connections

BaseSpace Sequence Hub and Illumina Proactive Domains

The following domains provide access from Universal Copy Service to BaseSpace Sequence Hub and Illumina Proactive. Some Enterprise addresses include a user-defined domain field.

Operating System Configurations

Illumina instruments are tested and verified to operate within specifications before shipping. Changes to settings after installation can create performance or security risks.

Configuration recommendations to mitigate performance and security risks:

• Configure a password that is at least 10 characters and use local ID policies. Keep a record of the password.
• Illumina does not keep customer login credentials. Unknown passwords can be reset with access to the system's root account or by booting into single-user mode. Otherwise, an Illumina representative can restore factory defaults, removing all data and potentially extending repair time.
• Maintain existing privileges for preconfigured users; make them unavailable as needed.
• The system assigns random internal IP addresses for communication with hardware components. Modifying these or the assignment method can cause hardware errors or loss of functionality.
• The control computer is designed for Illumina sequencing systems. Avoid using it for general-purpose computing (web browsing, email, document review) as this creates quality and security problems.

Services

NextSeq 1000/2000 Control Software utilizes Universal Copy Service, using the same credentials as the system login by default.

Mounting Network Drives

Do not share drives or folders from the instrument. Server Message Block (SMB), Common Internet File System (CIFS), and Network File System (NFS) are the only supported methods for persistent mounting of a network drive.

CentOS Updates

Instructions to install NextSeq 1000/2000 OS updates:

Install Updates Using Terminal

1. If NextSeq 1000/2000 Control Software is open, select Minimize Application.
2. Log in to ilmnadmin.
3. Select Applications.
4. Under Favorites, select Terminal.
5. To show available updates and packages, enter sudo yum check-update and press Enter.
6. Enter the ilmnadmin password when prompted.
7. Refresh the OS updates package database and install updates by entering sudo yum update and pressing Enter.

Install Updates Using the User Interface

1. If NextSeq 1000/2000 Control Software is open, select Minimize Application.
2. Log in to ilmnadmin.
3. Select Applications.
4. Under System Tools, select Software Updates.
5. A list displays available updates that can correct errors, eliminate security vulnerabilities, and provide new features. Select Install Updates.

Third-party Software

Illumina supports only the software provided at installation. Untested third-party software (e.g., Chrome, Java, Box, antivirus) can interfere with performance and security. For example, RSync can interrupt streaming, causing corrupt or missing sequencing data.

User Behavior

The instrument control computer is designed to operate Illumina sequencing systems. Do not consider it a general-purpose computer. Do not install additional software unless requested by an Illumina representative. For quality and security reasons, avoid using the control computer for web browsing, checking email, reviewing documents, or other unnecessary activities, as these can result in degraded performance or data loss.

Data Output and Storage

Storage Requirements for BaseSpace Sequence Hub

Illumina recommends uploading data to BaseSpace Sequence Hub. Approximate storage requirements per run based on run size:

User-Supplied Consumables and Equipment

The following consumables and equipment are used with the NextSeq 1000/2000. Refer to the NextSeq 1000 and 2000 Sequencing System Guide for more information.

Consumables for Sequencing

Consumables for Maintenance

*The instrument ships with one installed and one spare. Replacements are user-supplied when not under warranty.

Equipment

Technical Assistance

For technical assistance, contact Illumina Technical Support:

• Website: www.illumina.com
• Email: techsupport@illumina.com

Illumina Technical Support Telephone Numbers

Safety data sheets (SDSs) are available on the Illumina website at support.illumina.com/sds.html.

Product documentation is available for download from support.illumina.com.