NovaSeq 6000 ation
NovaSeq 6000 Sequencing System
Site Prep Guide
Introduction
3
Delivery and Installation
4
Laboratory Requirements
5
Storage Requirements for Reagent Kits
7
Lab Setup for PCR Procedures
8
Electrical Requirements
8
Uninterruptible Power Supply
11
Environmental Considerations
12
Network and Computer Security
13
Host Network Considerations
15
Data Output and Storage
18
User-Supplied Consumables and Equipment
20
Revision History
22
Technical Assistance
24
Document # 1000000019360 v06 January 2019 For Research Use Only. Not for use in diagnostic procedures.
ILLUMINA PROPRIETARY
NovaSeq 6000 Sequencing System Prep Guide
This document and its contents are proprietary to Illumina, Inc. and its affiliates ("Illumina"), and are intended solely for the contractual use of its customer in connection with the use of the product(s) described herein and for no other purpose. This document and its contents shall not be used or distributed for any other purpose and/or otherwise communicated, disclosed, or reproduced in any way whatsoever without the prior written consent of Illumina. Illumina does not convey any license under its patent, trademark, copyright, or common-law rights nor similar rights of any third parties by this document. The instructions in this document must be strictly and explicitly followed by qualified and properly trained personnel in order to ensure the proper and safe use of the product(s) described herein. All of the contents of this document must be fully read and understood prior to using such product(s). FAILURE TO COMPLETELY READ AND EXPLICITLY FOLLOW ALL OF THE INSTRUCTIONS CONTAINED HEREIN MAY RESULT IN DAMAGE TO THE PRODUCT(S), INJURY TO PERSONS, INCLUDING TO USERS OR OTHERS, AND DAMAGE TO OTHER PROPERTY, AND WILL VOID ANY WARRANTY APPLICABLE TO THE PRODUCT(S). ILLUMINA DOES NOT ASSUME ANY LIABILITY ARISING OUT OF THE IMPROPER USE OF THE PRODUCT(S) DESCRIBED HEREIN (INCLUDING PARTS THEREOF OR SOFTWARE). © 2019 Illumina, Inc. All rights reserved. All trademarks are the property of Illumina, Inc. or their respective owners. For specific trademark information, see www.illumina.com/company/legal.html.
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NovaSeq 6000 Sequencing System Prep Guide
Introduction
This guide provides specifications and guidelines for preparing your site for installation and operation of the Illumina® NovaSeqTM 6000 Sequencing System. u Laboratory space requirements u Electrical requirements u Environmental constraints u Computing requirements u User-supplied consumables and equipment
Safety Considerations
See the NovaSeq 6000 Sequencing System Safety and Compliance Guide (document # 1000000019357) for important information about safety considerations.
Additional Resources
The NovaSeq 6000 Sequencing System support pages on the Illumina website provide additional system resources. These resources include software, training, compatible products, and the following documentation. Always check support pages for the latest versions.
R es our ce
Custom Protocol Selector
NovaSeq 6000 Sequencing System Safety and Compliance Guide (document # 1000000019357)
RFID Reader Compliance Guide (document # 1000000002699)
NovaSeq Series Custom Primers Guide (document # 1000000022266)
NovaSeq 6000 Sequencing System Guide (document # 1000000019358)
D es cr i p t i on A wizard for generating customized end-to-end documentation that is tailored to the library prep method, run parameters, and analysis method used for the sequencing run. Provides information about operational safety considerations, compliance statements, and instrument labeling.
Provides information about the RFID reader in the instrument, including compliance certifications and safety considerations.
Provides information about replacing Illumina sequencing primers with custom sequencing prim e rs.
Provides an overview of instrument components, instructions for preparing sequencing consumables, instructions for operating the instrument, and maintenance and troubleshooting proc e du re s.
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NovaSeq 6000 Sequencing System Prep Guide
Delivery and Installation
An authorized service provider delivers the system, uncrates components, and places the instrument. Make sure that the lab space is ready before delivery. Floor loading risks related to instrument installation must be evaluated and addressed by building facility personnel.
CAUTION Only authorized personnel can uncrate, install, or move the instrument. Mishandling of the instrument can affect the alignment or damage instrument components. An Illumina representative installs and prepares the instrument. When connecting the instrument to a data management system or remote network location, make sure that the path for data storage is selected before the date of installation. The Illumina representative can test the data transfer process during installation.
CAUTION After your Illumina representative has installed and prepared the instrument, do not relocate it. Moving the instrument improperly can affect the optical alignment and compromise data integrity. If you must relocate the instrument, contact your Illumina representative.
Crate Dimensions and Contents
The NovaSeq 6000 System and components are shipped in one wooden crate (Crate #1) and one cardboard crate (Crate #2). Use the following dimensions to determine the minimum door width required to accommodate the shipping crates.
Meas ur ement H e i ght Width Depth Crated Weight
Crate #1 155 cm (61 in) 104 cm (41 in) 155 cm (61 in) 628 kg (1385 lbs)
Crate #2 84 cm (33 in) 122 cm (48 in) 102 cm (40 in) 176 kg (388 lbs)
NOTE For Crate #1, the forklift access points are on the depth side of the crate. Take this into consideration for doorway and elevator clearance when transporting the instrument in the crate.
NOTE The weight of the UPS and external battery pack for the UPS contained in Crate #2 can vary based on the model shipped.
u Crate #1 contains the instrument.
u Crate #2 contains five boxes with the following contents: u Box--Uninterruptible power supply (UPS), weight 46 kg (100 lbs) u Box--External battery pack for the UPS, weight 64 kg (140 lbs) u Box--Accessories, total weight 31 kg (68 lbs) u Monitor u Large used reagents bottle and small used reagents bottle u Instrument leak tray u Wire thaw racks
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u Wash flow cells u SBS wash cartridges u Cluster wash cartridges u Wireless keyboard and mouse, if appropriate for the region. In the absence of a wireless
keyboard, use a wired keyboard. u Box--Additional components
u Two buffer tray bottles that are individually packaged u Region-specific power cord u NovaSeq 6000 Sequencing System Guide (document # 1000000019358) u NovaSeq 6000 Sequencing System Safety and Compliance Guide (document # 1000000019357) u RFID Reader Compliance Guide (document # 1000000002699) u Box--Chimney adapter
Laboratory Requirements
Use the specifications and requirements provided in this section to set up your lab space.
Instrument Dimensions
Meas ur ement Height Width De pth Weight
Instrument Dimensions* 165.6 cm (65.2 in) 80.0 cm (31.5 in) 94.5 cm (37.2 in) 481 kg (1059 lb)
* The UPS system is not included in this dimension, additional space must be allocated.
Placement Requirements
Position the instrument to allow proper ventilation, access for servicing the instrument, and access to the power switch, power outlet, and power cord.
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u Position the instrument so that personnel can reach around the right side of the instrument to turn on or turn off the power switch. This switch is on the back panel adjacent to the power cord.
u Position the instrument so that personnel can quickly disconnect the power cord from the outlet.
u Make sure that the instrument is accessible from all sides using the following minimum clearance dimensions.
u Place the UPS on either side of the instrument. The UPS can be placed within the minimum clearance range of the instrument sides.
Access Front Sides Rear Top
Minimum Clearance
Allow at least 152.4 cm (60 in) in front of the instrument for opening the liquids compartment and to provide general lab access for movement of personnel around the lab.
Allow at least 76.2 cm (30 in) on each side of the instrument for access and clearance around the instrument. Instruments placed side by side only require 76.2 cm (30 in) total between the two instruments.
Allow at least 30.5 cm (12 in) behind the instrument placed next to a wall for ventilation and access. Allow at least 61 cm (24 in) between two instruments placed back-to-back.
Make sure that shelving and other obstructions are not above the instrument.
WARNING
Incorrect placement can reduce ventilation. Reduced ventilation increases heat output and noise output, which compromises data integrity and personnel safety.
Multisystem Installation Layout
The following diagram illustrates an example layout for a multisystem installation, including minimum spacing requirements.
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Vibration Guidelines
Keep the vibration level of the lab floor at the VC-A standard of 50 m/s for octave band frequencies of 8 80 Hz, or lower. This level is typical for labs. Do not exceed the ISO Operating Room (baseline) standard of 100 m/s for octave band frequencies of 880 Hz.
During sequencing runs, use the following best practices to minimize vibrations and ensure optimal performance:
u Place the instrument on a flat hard floor and keep the clearance area free of clutter.
u Do not place keyboards, used consumables, or other objects on top of the instrument.
u Do not install the instrument near sources of vibration that exceed the ISO Operating Room standard. For example: u Motors, pumps, shake testers, drop testers, and heavy air flows in the lab. u Floors directly above or below HVAC fans, and controllers, and helipads. u Construction or repair work on the same floor as the instrument.
u Keep sources of vibration such as dropped items and movement of heavy equipment at least 100 cm (39.4 in) from the instrument.
u Use only the touch screen, keyboard, and mouse to interact with the instrument. Do not directly impact the instrument surfaces during operation.
Storage Requirements for Reagent Kits
The NovaSeq 6000 Reagent Kit supports sequencing on a high-throughput system and can require significant storage space. Use the following specifications to determine storage requirements.
Storage Temperatures
A single flow cell run requires 1 of each of the following items. A dual flow cell run requires 2 of each item.
Item Buffer cartridge Cluster cartridge Flow cell Library tube SBS cartridge
Storage Temperature 15°C to 30°C -25°C to -15°C 2°C to 8°C 15°C to 30°C -25°C to -15°C
Light Sensitivity
The SBS and buffer cartridges contain reagents that are sensitive to light. If you remove the SBS cartridge from the packaging for storage, make sure that it is stored in the dark with no sources of light. Keep the buffer container packaged until use.
Reagent Kit Dimensions
The following table provides quantities and dimensions for the packaged components in a NovaSeq 6000 Reagent Kit. The specifications are the same regardless of kit size.
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Table 1 Dimensions of Kit Components
Kit Component
Quantity
Le ngt h
Buffer cartridge
1
42.2 cm (16.6 in)
Cluster cartridge
1
29.5 cm (11.6 in)
Flow cell
1
35.6 cm (14 in)
Library tube
1
4.1 cm (1.6 in)
SBS cartridge
1
30 cm (11.8 in)
Width 20.6 cm (8.1 in) 13 cm (5.1 in) 20.3 cm (8 in) 2.3 cm (0.9 in) 12.4 cm (4.9 in)
H e i ght 21.1 cm (8.3 in) 9.4 cm (3.7 in) 2.8 cm (1.1 in) 12.4 (4.9 in) 11.2 cm (4.4 in)
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 before you begin work in the lab. PCR products can contaminate reagents, instruments, and samples, delaying normal operations and causing inaccurate results.
Pre-PCR and Post-PCR Areas
Use the following guidelines to avoid cross-contamination. u Establish a pre-PCR area for pre-PCR processes. u Establish a post-PCR area for processing PCR products. u Do not use the same sink to wash pre-PCR and post-PCR materials. u Do not use the same water purification system for pre-PCR and post-PCR areas. u Store supplies used for pre-PCR protocols in the pre-PCR area. Transfer them to the post-PCR area as
needed.
Dedicate Equipment and Supplies
u Do not share equipment and supplies between pre-PCR and post-PCR processes. Dedicate a separate set of equipment and supplies in each area.
u Establish dedicated storage areas for consumables used in each area.
Electrical Requirements Power Specifications
Ty p e Line Voltage Peak Power Consumption
S p eci fi cat i on 200240 VAC at 50/60 Hz 2500 Watts
For 200240 Volts AC, your facility must be wired with a minimum 15 Amp grounded line with proper voltage. An electrical ground is required. If the voltage fluctuates more than 10%, a power line regulator is required.
The instrument must be connected to a dedicated circuit that must not be shared with any other equipment.
For more information, see the NovaSeq 6000 Sequencing System Safety and Compliance Guide (document # 1000000019357) .
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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. The protective earth connection on the power cord must be in good working condition when using this device.
Power Cords
The instrument comes with an international standard IEC 60320 C20 receptacle, and is shipped with a region-specific power cord. To obtain equivalent receptacles or power cords that comply with local standards, consult a third-party supplier such as Interpower Corporation (www.interpower.com). All power cords are 2.5 m (8 ft) in length.
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.
Table 2 Power Cord Requirements of Selected Regions
R egi on
Shipped Power Cord
A u stra lia
AS 3112 SAA Male to C19, 15 Amps
Electrical Supply Socket 230 VAC, 15 Amps 15 Amp Type I
Bra zil
NBR14136 Plug to C19, 16 Amps
220 VAC, 16 Amps NBR 14136 Type N
China
GB2099 to C19, 16 Amps
Eu rope a n Union¹
Schuko CEE 7 (EU1-16p) to C19, 16 Amps
220 VAC, 16 Amps GB 1002, GB 2099, Type I
220-240 VAC, 16 Amps
Schuko CEE 7/3
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R egi on India
Shipped Power Cord IS1293 to C19, 16 Amps
Isra e l
IEC 60320 C19, 16 Amps
Ja pa n
NEMA L6-30P, 30 Amps
New Zealand
AS 3112 SAA Male to C19, 15 Amps
N orth A m e ric a
NEMA L6-20P to C19, 20 Amps
S in ga pore
IEC60309 316P6 to C19, 16 Amps
South Africa SANS 164-1 to C19, 16 Amps
Electrical Supply Socket 230 VAC, 16 Amps BS546A Type M
230 VAC, 16 Amps SI 3216 Amp Type H
200 VAC, 30 Amps NEMA L6-30R
230 VAC, 15 Amps Dedicated 15 Amp Type I
208 V, 16 Amps
NEMA L6-20R
230-250 VAC, 16 Amps
IEC60309 316C6
230 VAC, 16 Amps BS546A Type M
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R egi on S w itze rla n d
Shipped Power Cord SEV 1011 Type 23 Plug J, 16 Amps
Un ite d Kingdom
IEC60309 316P6 to C19, 16 Amps
Electrical Supply 230 VAC, 16 Amps
Socket
SEV 1011 Type 23 J soc ke t
230-250 VAC, 16 Amps
IEC60309 316C6
¹ Excepting Switzerland and the United Kingdom.
NOTE Alternatively, all regions can use IEC 60309.
Fuses
The instrument contains no user-replaceable fuses.
Uninterruptible Power Supply
The following specifications apply to the worldwide UPS and battery that ships with the instrument. For countries that require a different model of UPS and battery, and alternatives, see Country-Specific Uninterruptible Power Supply. u UPS--APC Smart-UPS X 3000 Rack/Tower LCD 200-240V, Model # SMX3000RMHV2U u Battery--APC Smart-UPS X, Model # SMX120RMBP2U
S p eci fi cat i on Maximum Output Power Input Voltage (nominal) Input Frequency Input Connection Typical Run Time (Average Power of 1.8 kW) Typical Run Time (Peak Power of 2.5 kW) Weight Dimensions (Tower format: H × W × D)
UPS With Battery 2700 Watts*/ 3000 VA 200240 VAC 50/60 Hz IEC-60320 C20 51 minutes
34 minutes
95 kg (210 lb) (43.2 cm × 66.7 cm × 17 cm) (17 in × 26.26 in × 6.72 in)
* The UPS requires up to a maximum of 330 Watts to charge batteries and perform other internal functions. 2700 Watts is available for output during this time.
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Country-Specific Uninterruptible Power Supply
Illumina supplies the following country-specific UPS and batteries. Unless indicated, only one battery is required.
C ount r y Columbia India Ja pa n Mexico South Korea Thailand
UPS Model # SRT3000RMXLW-IEC SUA3000UXI SRT5KXLJ SRT3000RMXLW-IEC SRT3000RMXLW-IEC SRT3000RMXLW-IEC
Battery Model # SRT96RMBP SUA48XLBP (2) SRT192BPJ SRT96RMBP SRT96RMBP SRT96RMBP
For additional specification information, see the APC website (www.apc.com).
NOTE Exact UPS and battery options are subject to availability and can change without notice.
Environmental Considerations
Element Te m pe ra tu re * Humidity* Ele va tion Air Quality
Vibra tion
S p eci fi cat i on
Maintain a lab temperature of 19°C to 25°C (22°C ±3°C). Failure to operate the instrument within the temperature range can degrade performance or cause a run to fail.
Maintain a noncondensing relative humidity between 2080%. Preferred range is a relative humidity between 2060%.
Locate the instrument at an elevation below 2000 meters (6500 feet).
Operate the instrument in an indoor environment with air particulate cleanliness levels per ISO 9 (ordinary room air), or better. Keep the instrument away from sources of dust.
Limit the continuous vibration of the lab floor to ISO operating room level (baseline), or be tte r. During a sequencing run, limit intermittent disturbances or shocks to the floor near the instrument. Do not exceed ISO office level.
*Avoid a combination of high temperature and high humidity. For example, 25°C and 80% relative humidity.
Noise Output
Noise Output (dB) < 75 dB
Distance From Instrument 1 meter (3.3 feet)
Heat Output
Peak Power Consumption 2500 Watts
Thermal Output
Maximum 8530 BTU/h Average 6000 BTU/h
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Venting
A 10 inches round vertical chimney vents 60% of instrument heat output. You can vent to the room or connect the chimney to a user-supplied duct. Use the following guidelines for venting ducts. u Flexible ducting is preferred. u Avoid bending flexible ducts where possible. Keep bends in flexible ducts to a minimum. u Flexible ducts with bends must maintain the 10 inch diameter of the chimney at all points. u Remove kinks or other restrictions to the airflow. u Rigid ducting can be used. Use of rigid ducting can require Illumina personnel to move the instrument for
service. u Use the shortest length of ducting possible. u Route to a space with sufficient ventilation to prevent airflow restriction or backup into the instrument.
CAUTION Failure to follow these guidelines can impact instrument performance and can cause run failures. Chimney airflow is 450 CFM. Chimney air temperature is up to 12°C higher than ambient temperature. Figure 1 Chimney Placement for Venting
Bulk Used Reagent Handling
The NovaSeq 6000 System system is equipped to dispense used reagent buffer to a customer-supplied bulk container for separate processing or handling. The supplied external used reagent tubes included in the accessory kit are 5 meters long, and connect to the left rear of the instrument. Illumina only supports external used reagent collection with the supplied tubes. Each tube contains the buffer waste from a single flow cell position, and must be routed individually to the bulk container. The container must be placed within 5 meters of the instrument. The aperture must be at a height of 1000 mm or less from the floor.
Network and Computer Security
The following sections provide guidelines for maintaining network and computer security. For information on recommended configurations, see Operating System Configurations on page 17.
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Compute Engine Security
The Compute Engine (CE) is an ancillary compute system that runs the camera interface board (CIB), BaseSpace Sequence Hub software. For security purposes, the Compute Engine is not user-accessible. However, it interfaces with the instrument control computer, which runs the control software and service software.
Linux Security
The Compute Engine runs on the instrument and uses a Linux-based operating system. To protect the system, Linux uses security configurations that cannot be disabled. Other features of Linux include SecurityEnhanced Linux (SELinux).
Compute Engine Connection
The Compute Engine uses the IP address 169.254.0.1 to interface with the control computer.
Control Computer Security
The control computer combines user-supplied antivirus software and the following configurable options for enhanced security. u Enhanced Mitigation Experience Toolkit (EMET)--Prevents the exploitation of software vulnerabilities. u Software restriction policies--Increase the reliability, integrity, and manageability of computers in a
domain. By restricting configurations, only identified applications can run. If necessary, EMET and software restriction policies can be disabled. Software restriction polices are configurable. For more information, see the NovaSeq 6000 Sequencing System Guide (document # 1000000019358).
Antivirus Software
An antivirus software of your choice is highly recommended to protect the instrument control computer against viruses. To avoid data loss or interruptions, configure the antivirus software as follows: u Set for manual scans. Do not allow automatic scans. u Perform the manual scans only when the instrument is not in use. u Set updates to download without user authorization, but not install. u Do not make updates during instrument operation. Make updates only when the instrument is not
running and when it is safe to reboot the control computer. u Do not reboot the computer automatically upon update. u Exclude the application directory and data drives from any real-time file system protection. Apply this
setting to the C:\Illumina and Z:\ilmn directories. u Turn off Windows Defender. This Windows product can affect the operating system resources used by
Illumina software.
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Host Network Considerations
The NovaSeq 6000 Sequencing System is designed for use with a network, regardless of whether runs are configured for BaseSpace Sequence Hub. The system is not intended to store run data. Therefore, performing a run in standalone mode requires a network connection to transfer run data to a network location. The following operations require an external internet connection, even if BaseSpace Sequence Hub is not used. u Updating the control software. u Uploading instrument performance data to Illumina. u Remote assistance from Illumina Technical Support. Do not save run data to a local hard drive. The system hard drive is intended for temporary storage before data are transferred automatically. Data saved on the hard drive that are not used by the current run can compromise performance.
Network Connections
Illumina does not install or provide technical support for network connections. Review network maintenance activities for potential compatibility risks with the NovaSeq 6000 Sequencing System. Use the following guidelines to install and configure a network connection: u Use a dedicated 1 gigabit connection between the instrument and data management system. Make this
connection directly or through a network switch. u Required bandwidth for a connection is:
u 200 Mb/s/instrument for internal network uploads. u 200 Mb/s/instrument for BaseSpace Sequence Hub network uploads. u 5 Mb/s/instrument for Instrument Operational Data uploads. u Switches must be managed. u Network equipment such as switches must have a minimum of 1 gigabit per second. u Calculate the total capacity of the workload on each network switch. The number of connected instruments and ancillary equipment, such as a printer, can impact capacity. u If possible, isolate sequencing traffic from other network traffic. u Cables must be CAT-5e, or better, Illumina recommends the use of CAT-6. A shielded network cable that is 3 meters (9.8 feet) long is provided with the instrument for network connections.
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Control Computer Connections
For the system to function properly, reserve the IP ranges 169.254/16 and IPv6 fddc:65e5:66fa::*. Figure 2 Network Illustration
NOTE The CE is not visible on the host network. The following tables describe the network ports and domains of the control computer. Use these tables as a reference when setting up your network.
Internal Connections
C onne c t i on D oma i n
Port
Value localhost:*
5555 8081 8080 8090 22, 80, 111, 443, 623, 2049, 5900, 8889, 9980, fddc:65e5:66fa::1/48, fddc:65e5:66fa::2/48
Pur p os e All ports for localhost-to-localhost communication, which are needed for interprocess communication Hardware controller interface Real-Time Analysis NovaSeq Control Software Universal Copy Service Data transfer
Outbound Connections
The following sections provide domain and IP address information for configuring access to BaseSpace Sequence Hub domains, Illumina Proactive, software updates, and uploads of run and performance data.
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BaseSpace Sequence Hub 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. This custom field is reserved with {domain}.
Instance US Enterprise
EU Enterprise US Basic and Professional
EU Basic and Professional
Address {domain}.basespace.illumina.com {domain}.api.basespace.illumina.com ba se spa c e -da ta -e a st.s3-e xte rn a l-1.a m a zon a w s.c om basespace-data-east.s3.amazonaws.com in stru m e n ts.sh .ba se spa c e .illu m in a .c om {domain}.euc1.sh.basespace.illumina.com {domain}.api.euc1.sh.basespace.illumina.com e u c 1-prd-se q-h u b-da ta -bu c ke t.s3-e u -c e n tra l-1.a m a zon a w s.c om in stru m e n ts.sh .ba se spa c e .illu m in a .c om basespace.illumina.com api.basespace.illumina.com ba se spa c e -da ta -e a st.s3-e xte rn a l-1.a m a zon a w s.c om basespace-data-east.s3.amazonaws.com in stru m e n ts.sh .ba se spa c e .illu m in a .c om euc1.sh.basespace.illumina.com api.euc1.sh.basespace.illumina.com e u c 1-prd-se q-h u b-da ta -bu c ke t.s3-e u -c e n tra l-1.a m a zon a w s.c om in stru m e n ts.sh .ba se spa c e .illu m in a .c om
IP Addresses and Ports
Use the following IP address and port connections for BaseSpace Sequence Hub, Illumina Proactive configuration, uploads, and software updates.
BMC NFS
CE Hardware Controllers
TCP 22,80,443,623,5900,8889 111,2049
22,9980 n/a
UDP 623 111,2049
n/a n/a
IP
169.254.0.2 fddc:65e5:66fa::2/48 fddc:65e5:66fa::1/48 169.254.0.1 169.254.x.x/16
Operating System Configurations
Illumina instruments are tested and verified to operate within specifications before shipping. After installation, changes to settings can create performance or security risks.
The following configuration recommendations mitigate performance and security risks for the operating system:
u Configure a password that is at least 10 characters, and use local ID policies for additional guidance. Keep a record of the password.
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u Illumina does not keep customer login credentials, and unknown passwords cannot be reset. u An unknown password requires that an Illumina representative restore the factory default, which
removes all data from the system and extends the necessary support time. u When connecting to a domain with Group Policy Objects (GPOs), some settings might affect the
operating system or instrument software. If the instrument software operates incorrectly, consult your facility IT administrator about possible GPO interference. u Use the Windows firewall or a network firewall (hardware or software) and disable the Remote Desktop Protocol (RDP). For more information on firewalls and RDP, see the Illumina Security Best Practices Guide (Pub No. 970-2016-016). u Maintain administrative privileges for users. Illumina instrument software is configured to allow user permissions when the instrument is shipped. u The system has fixed internal IP addresses, which can cause system failure when conflicts occur. u The control computer is designed to operate Illumina sequencing systems. Web browsing, checking email, reviewing documents, and other nonsequencing activity creates quality and security problems.
Windows Updates
To secure your data, it is recommended that all Windows critical security updates are applied on a regular schedule. The instrument must be idle when updates are applied as some updates require a full system reboot. General updates can put the system operating environment at risk and is not supported. If security updates are not possible, alternatives to turning on Windows Update include: u More robust firewalling and network isolation (virtual LAN). u Network isolation of network attached storage (NAS), which still allows for data to sync to the network. u Local USB storage. u User behavior and management to avoid improper use of the control computer and ensure the
appropriate permission-based controls. For more information on Windows Update alternatives, contact Illumina Technical Support.
Third-party Software
Illumina supports only the software provided at installation. Chrome, Java, Box, and other third-party software are untested and can interfere with performance and security. For example, RoboCopy interrupts streaming performed by the control software suite. The interruption can cause corrupt and missing sequencing data.
User Behavior
The instrument control computer is designed to operate Illumina sequencing systems. Do not consider it a general-purpose computer. For quality and security reasons, do not use the control computer for web browsing, checking email, reviewing documents, or other unnecessary activity. These activities can result in degraded performance or loss of data.
Data Output and Storage
Storage Requirements for BaseSpace Sequence Hub
Illumina recommends uploading data to BaseSpace Sequence Hub. Based on run size, BaseSpace Sequence Hub requires the following storage per run.
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Flow Cell Type NovaSeq 6000 System SP 300 Cycle NovaSeq 6000 System SP 500 Cycle NovaSeq 6000 System S1 300 Cycle NovaSeq 6000 System S2 300 Cycle NovaSeq 6000 System S4 300 Cycle
Single Flow Cell Run 0.10 TB 0.16 TB 0.37 TB 0.73 TB 2.19 TB
Dual Flow Cell Run 0.20 TB 0.32 TB 0.73 TB 1.43 TB 4.35 TB
Locally Attached Storage or Network Requirements
The following table provides file types and minimum storage requirements for a sequencing run and its secondary analysis. The table lists requirements for a dual flow cell run by each flow cell type.
NOTE For single flow cell runs, the minimum space requirements are half of those in the table. Alternate run configurations have different storage requirements.
File Type CBCL Interop folder FASTQ BAM gVCF and VCF
SP 300 Cycle 235 GB 0.6 GB 285 GB 265 GB 7 GB
SP 500 Cycle 392 GB 1 GB 475 GB 442 GB 11.6 GB
S1 300 Cycle 470 GB 1.2 GB 570 GB 530 GB 14 GB
S2 300 Cycle 930 GB 2.3 GB 1125 GB 1050 GB 28 GB
S4 300 Cycle 2800 GB 7.0 GB 3387 GB 3160 GB 84 GB
NOTE Map mounted storage locations using the full UNC path. Do not use letters or symbolic links.
Example Data Usage
The following table provides an example for building an infrastructure that supports data generated with the NovaSeq 6000 Sequencing System. The table lists data storage options for whole-genome sequencing analysis with BaseSpace Sequence Hub. The examples assume that a dual flow cell, 300 cycle run with S2 flow cells generates 2 TB of data at a usage rate of 10 runs per month. The SP, S1, and S4 data points are extrapolated from the S2 assumptions. Both the SP and S1 flow cells complete in approximately half the time of an S2 flow cell. For a 500 cycle run with SP flow cells at a usage rate of 10 runs per month, 0.25 TB of data is generated. Adjust the numbers in the table for a lower rate of use. If you expect to perform repeat analysis of data sets, increase storage proportionately. Because actual data retention is subject to local policies, confirm conditions before calculating storage needs.
NOTE Run sizes vary depending on multiple factors including length and the percentage of pass filter (PF). The numbers provided are intended to be a guide to the relative range of the data footprint.
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File Type
BAM
BAM
VCF and gVC F VCF and gVC F
Ti me Pe r i od Monthly
Annual
Monthly
Annual
Number of Runs
10 runs/1 month per system*
120 runs/1 year per system
10 runs/1 month per system
120 runs/1 year per system
* Storage for data backup and archival is not included.
SP 300 Cycle 2.65 TB
31.8 TB
0.07 TB
0.84 TB
SP 500 Cycle
4.42 TB
S1 300 Cycle
14 TB
53.04 TB 163 TB
0.12 TB
0.3 TB
1.39 TB
3.6 TB
S2 300 Cycle 14 TB
168 TB
0.3 TB
3.6 TB
S4 300 Cycle 42 TB
504 TB
0.9 TB
10.8 TB
User-Supplied Consumables and Equipment
The following user-supplied consumables and equipment are used for consumable preparation, sequencing, and system maintenance. For more information, see the NovaSeq 6000 Sequencing System Guide (document # 1000000019358).
Consumables
C ons umab l e 1 N NaOH 10 mM Tris-HCl, pH 8.5
400 mM Tris-HCl, pH 8.0
Centrifuge bottle, 500 ml Centrifuge tube, 30 ml Disposable gloves, powderf re e Isopropyl alcohol wipes, 70% or Ethanol alcohol wipes, 70% Lab tissue, low-lint
Microcentrifuge tube, 1.5 ml
NaOCl, 5% Pipette tips, 20 l Pipette tips, 200 l Pipette tips, 1000 l Reagent or spe c troph otom e tric -gra de isopropyl alcohol (99%), 100 ml bottle Tween 20
Supplier General lab supplier General lab supplier
General lab supplier
General lab supplier General lab supplier General lab supplier
Pur p os e Diluting to 0.2 N for denaturing libraries. Diluting libraries and an optional PhiX control before denaturation. Neutralizing libraries and an optional PhiX control after denaturation. Diluting Tween 20 for a maintenance wash. Diluting NaOCl for a maintenance wash. General purpose.
VWR, catalog # 95041-714, or equivalent General lab supplier
VWR, catalog # 21905-026, or equivalent
VWR, catalog # 20170-038, or equivalent
Sigma-Aldrich, catalog # 239305
General lab supplier
General lab supplier
General lab supplier
General lab supplier
Cleaning components before a run and general pu rpose .
Drying the flow cell stage and general purpose.
Combining volumes when diluting NaOH and libra ry. Performing a maintenance wash. Pipetting for diluting and loading libraries. Pipetting for diluting and loading libraries. Pipetting for diluting and loading libraries. Cleaning optics components periodically and support the objective cleaning cartridge.
Sigma-Aldrich, catalog # P7949
Performing a maintenance wash.
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C ons umab l e
Water, laboratory-grade (see Guidelines for LaboratoryGrade Water on page 21)
[NovaSeq Xp workflow] One of the following kits: · NovaSeq Xp 2-Lane Kit · NovaSeq Xp 4-Lane Kit
[NovaSeq Xp workflow] 0.5 ml and 1.7 ml tubes
[NovaSeq Xp workflow] [Optional] One of the following manifold packs: · NovaSeq Xp 2-Lane
Manifold Pack · NovaSeq Xp 4-Lane
Manifold Pack
[Optional] PhiX Control v3
Supplier General lab supplier
Illu m in a : · Catalog # 20021664 · Catalog # 20021665 General lab supplier Illu m in a : · Catalog # 20021666 · Catalog # 20021667
Illumina, catalog # FC-110-3001
Pur p os e Diluting NaOH for denaturing libraries. Diluting Tween 20 and sodium hypochlorite for a maintenance wash. Manually loading libraries onto a flow cell: · Two-lane kit for SP, S1, and S2 flow cells · Four-lane kit for S4 flow cells Required for ExAmp mixing.
Spare NovaSeq Xp manifolds for manually loading libraries onto a flow cell.
Spiking in PhiX control.
Guidelines for Laboratory-Grade Water
Always use laboratory-grade water or deionized water to perform instrument procedures. Never use tap water. Use only the following grades of water or equivalents: u Deionized water u Illumina PW1 u 18 Megohms (M) water u Milli-Q water u Super-Q water u Molecular biology grade water
Equipment
Item Freezer, -25°C to -15°C Graduated cylinder, 500 ml, sterile Ice bucket Pipette, 20 µl Pipette, 200 µl Pipette, 1000 µl Refrigerator, 2°C to 8°C Tub, water baths* [NovaSeq Xp workflow] NovaSeq Xp Flow Cell Dock
Source General lab supplier General lab supplier General lab supplier General lab supplier General lab supplier General lab supplier General lab supplier General lab supplier Illumina, catalog # 20021663
* Use a tub that can accommodate two reagent cartridges and the appropriate water level. For example, (61 cm × 91.4 cm × 25.4 cm)(24 in × 36 in × 10 in).
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Revision History
Document Document # 1000000019360 v06 Document # 1000000019360 v05
Document # 1000000019360 v04 Document # 1000000019360 v03
Document # 1000000019360 v02
Date Ja n u a ry
2019 September
2018
July 2018 May 2018
September 2017
Description of Change
Updated information for SP 300 cycle and SP 500 cycle flow cells. Corrected link to the support site.
Updated power specification information with requirement for a dedicated circuit for the instrument. Updated venting requirements to prevent overheating of the instrument. Noted to map mounted storage locations using the full UNC path.
Corrected Compute Engine connection IP address. Corrected reserve IP addresses for computer connections.
Noted forklift access points for the crate that contains the instrument. Updated country-specific universal power supply information: · Removed Brazil and Taiwan UPS information. · Corrected part number for Japan UPS. Data output and storage information: · Updated BaseSpace storage requirements for S2 flow dual cell run. · Updated local storage requirement for dual flow cell runs.
Added data output and storage information for S1 and S4 flow cells. Updated venting information: · Flexible ducting is preferred. · Added graphic to illustrate chimney placement for venting. Added reference to NovaSeq 6000 Sequencing System Guide (document # 1000000019358) in the Control Computer Security, for information on configuring software restriction policies. Added descriptive information to instrument placement requirements table. Updated outbound connection information: · Added BaseSpace US and EU domains · Added IP address and port connection information for BaseSpace,
instrument performance data, and software updates. Updated the Network Illustration. Updated operating system configuration information for automatic updates in Windows. Updated recommendations for securing data in Windows. Corrected Compute Engine connection IP address. Added reagent or spectrophotometric-grade isopropyl alcohol (99%) consumable.
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NovaSeq 6000 Sequencing System Prep Guide
Document Document # 1000000019360 v01
Document # 1000000019360 v00
Date April 2017
Ja n u a ry 2017
Description of Change
Added Custom Protocol Selector to the list of Additional Resources. Updated packaging changes for crate contents and weights. Updated instrument information: · Updated H × W × D dimensions and weight. · Noted that building facility personnel are responsible for evaluating floor
loading risk for instrument installation. Updated instrument placement requirements: · Updated access requirements. · Added Multi-system Installation Layout section. Updated environmental information: · Noted to avoid a combination of 25°C and 80% relative humidity. · Added information on how to dispense used waste buffer in bulk. Updated line voltage frequency to 50/60 Hz. Updated power cord information: · Specified additional power cords by region. · Corrected the image of the NEMA L6-20P power plug. Updated universal power supply information: · Added information for countries that require a different model of UPS and
ba tte ry. · Noted that exact UPS and battery options are subject to availability and can
change without notice. · Added H × W × D dimensions to worldwide UPS/Battery table · Specified an additional 300 Watts of power consumption for internal
UPS functions. · Removed third party UPS reference. Updated chimney vent dimension to 10 inches vertical round. Corrected Outbound Connections, Domain Values table.
Initial release.
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NovaSeq 6000 Sequencing System Prep Guide
Technical Assistance
For technical assistance, contact Illumina Technical Support.
Website: Email:
www.illumina.com te c h su pport@ illu m in a .c om
Illumina Customer Support Telephone Numbers
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R egi onal
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+45 89871156 +358 974790110 +33 170770446 +49 8938035677
+353 016950506 +39 236003759
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+47 21939693
+34 800300143 +46 200883979 +41 800200442
+44 2073057197
Safety data sheets (SDSs)--Available on the Illumina website at support.illumina.com/sds.html.
Product documentation--Available for download in PDF from the Illumina website. Go to support.illumina.com, select a product, then select Documentation & Literature.
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Document # 1000000019360 v06
Illumina 5200 Illumina Way San Diego, California 92122 U.S.A. +1.800.809.ILMN (4566) +1.858.202.4566 (outside North America) t e c hsupport @i l l um i na . c om www.illumina.com
For Research Use Only. Not for use in diagnostic procedures. © 2019 Illumina, Inc. All rights reserved.
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