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illumina NovaSeq 6000 Manual

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NovaSeq 6000
Sequencing System Guide
Document # 1000000019358 v07 Material # 20023471
April 2018
For Research Use Only. Not for use in diagnostic procedures.
ILLUMINA PROPRIETARY

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  • Page 1 NovaSeq 6000 Sequencing System Guide Document # 1000000019358 v07 Material # 20023471 ILLUMINA PROPRIETARY April 2018 For Research Use Only. Not for use in diagnostic procedures.
  • Page 2 NovaSeq 6000 Sequencing System 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.
  • Page 3 1000000019358 v07 Added a symbol descriptions table for symbols on the consumables or consumable packaging. Added information about the Illumina Proactive monitoring service in the Run Setup Modes section. Added information about the NovaSeq LIMS API. Updated software descriptions to NovaSeq Control Software v1.4.0 Updated typical number of reads passing filter for S2 flow cells.
  • Page 4 Reorganized kit overview information in a Kits and Accessories chapter. This chapter covers configurations, components, and compatibility labeling for the reagent and library loading kits. Added the NovaSeq 6000 Reagent Kit to the user-supplied consumables. Updated pool and denature library instructions to include information for S1 and S4 flow cells.
  • Page 5 Description of Change Material # 20018871 April Added the following information: Document # • Illumina-supplied consumables required for a run. 2017 • Storage conditions of reagent kit components. 1000000019358 v02 • Recommendations for library loading concentration. • NaOH dilution for two flow cells.

  • Page 6: Table Of Contents

    Table of Contents Chapter 1 Overview Introduction Additional Resources Sequencing Overview Sequencing Workflow Instrument Components Chapter 2 Kits and Accessories Kits Overview Reagent Kit Components NovaSeq Xp Kit Components NovaSeq Xp Flow Cell Dock Symbol Descriptions Chapter 3 Getting Started Start the Instrument Configure Settings User-Supplied Consumables and Equipment...
  • Page 7 NovaSeq 6000 Sequencing System Guide Chapter 7 Maintenance Preventive Maintenance Perform a Maintenance Wash Staggered Start of Runs on Flow Cell A and Flow Cell B Software Updates Appendix A Troubleshooting Troubleshooting Resources Troubleshooting Files Pre-Run Check Errors Process Management Troubleshooting...

  • Page 8: Chapter 1 Overview

    Adjustable output—The NovaSeq 6000 is a dual flow cell system with a broad output range. Sequence one flow cell, or sequence two flow cells with different read lengths simultaneously. Mix and match three types of flow cells and different read lengths.

  • Page 9: Additional Resources

    NovaSeq 6000 Sequencing System support pages on the Illumina website for software downloads, training resources, information about compatible Illumina products, information on recycling of consumables and packaging, and the most recent versions of this system guide and the following documentation. Always check support pages for the latest versions.

  • Page 10: Sequencing Workflow

    An instrument wash begins automatically when sequencing is complete. Library Loading Methods Libraries are loaded onto a NovaSeq 6000 Flow Cell using one of the following two methods, depending on the workflow selected. Setting up a sequencing run differs based on the workflow. Make sure that you always follow the instructions for your method.
  • Page 11 NovaSeq 6000 Sequencing System Guide Table 1 Library Loading Methods Loading Volume Library Pool Loading and ExAmp Individual Lane Addressability and Workflow S1–S2–S4 Mixing Method Data Analysis Modes (µl) Standard A single library pool is loaded into the A single library pool is distributed, and 150–225–465 µl...

  • Page 12: Instrument Components

    NovaSeq 6000 Sequencing System Guide Instrument Components The NovaSeq 6000 Sequencing System comprises a touch screen monitor, a status bar, a power button with adjacent USB ports, and three compartments. Figure 1 External Components A Touch screen monitor—Displays the control software interface for system configuration and run setup and monitoring.
  • Page 13 NovaSeq 6000 Sequencing System Guide Figure 2 Flow Cell Stage A Side A flow cell holder B Side B flow cell holder C Flow cell clamp (one of four per side) D Optical alignment target The software controls the opening and closing of the flow cell compartment door. The door opens automatically to load a flow cell for a run or maintenance wash.
  • Page 14 To demonstrate proper unloading and loading of consumables, NVCS plays instructional videos during run setup. Real-Time Analysis (RTA)—Performs image analysis and base calling during a run. NovaSeq 6000 uses RTA3, which incorporates architecture, security, and other feature enhancements to optimize performance.
  • Page 15 NovaSeq 6000 Sequencing System Guide Table 2 NVCS Status Icons Status Status Name Description Icon Status okay System is normal. Processing System is processing. Warning A warning has occurred and attention is required. Warnings do not stop a run or require action before proceeding.
  • Page 16 NovaSeq 6000 Sequencing System Guide Process Icon Description BaseSpace Files are being uploaded to BaseSpace Sequence Hub. All files are uploaded to BaseSpace Sequence Hub. Not applicable because the run is not configured to upload to BaseSpace Sequence Hub or the upload status is unknown.

  • Page 17: Chapter 2 Kits And Accessories

    Symbol Descriptions Kits Overview Performing a run on the NovaSeq 6000 requires a NovaSeq 6000 Reagent Kit. The NovaSeq Xp workflow also requires a NovaSeq Xp Kit. These kits are available in the following configurations. For a complete list of items needed for a run, see...

  • Page 18: Reagent Kit Components

    Library Tube The NovaSeq 6000 library tube is a 16 mm tube that fits into position #8 of the cluster cartridge. Position #8 is labeled Library Tube and circled in orange for easy identification. The tube has a threaded cap that allows storage of libraries when necessary.
  • Page 19 NovaSeq 6000 Sequencing System Guide Flow Cell The NovaSeq 6000 flow cell is a patterned flow cell encased in a cartridge. The flow cell is a glass-based substrate containing billions of nanowells in an ordered arrangement, which increases the number of output reads and sequencing data.
  • Page 20 C Gasket (one of four) Buffer, Cluster, and SBS Cartridges The NovaSeq 6000 buffer, cluster, and SBS cartridges have foil-seal reservoirs prefilled with reagents, buffers, and wash solution. One of each cartridge type is included with the reagent kit. The cartridges load directly onto the instrument, and are color-coded and labeled to reduce loading errors.

  • Page 21: Novaseq Xp Kit Components

    NovaSeq 6000 Sequencing System Guide Cluster Cartridge Reservoirs Removable Reservoir A denaturation reagent in position #30 contains formamide, which is an organic amide and reproductive toxin. To facilitate safe disposal of any unused reagent after the sequencing run, this reservoir is removable.

  • Page 22: Novaseq Xp Flow Cell Dock

    NovaSeq 6000 Sequencing System Guide Table 8 NovaSeq Xp Kit Components Quantity Kit Component Storage Temperature DPX1 -25°C to -15°C DPX2 -25°C to -15°C DPX3 -25°C to -15°C NovaSeq Xp Manifold Leave with the kit, or store at room temperature.

  • Page 23: Symbol Descriptions

    NovaSeq 6000 Sequencing System Guide Figure 9 NovaSeq Xp Flow Cell Dock A Overhangs (under the bracket) to guide loading B Springs to align the flow cell C Cutouts to hold the NovaSeq Xp manifold arms D Clamp to secure the flow cell and NovaSeq Xp manifold Symbol Descriptions The following table describes the symbols on the consumable or consumable packaging.
  • Page 24 NovaSeq 6000 Sequencing System Guide Symbol Description Indicates the serial number. Indicates that protection from light or heat is required. Store away from sunlight. Indicates a health hazard. Indicates a hazard warning. Storage temperature range in degrees Celsius. Store the consumable within the indicated range.²...

  • Page 25: Chapter 3 Getting Started

    Chapter 3 Getting Started Start the Instrument Configure Settings User-Supplied Consumables and Equipment Start the Instrument Switch the toggle power switch on the back of the instrument to the | (on) position. Figure 10 Power Switch Location Wait until the power button on the right side of the instrument glows blue, and then press it. Figure 11 Power Button Location When the operating system is loaded, log on to Windows using the username and password for your site.
  • Page 26 The name of the setting in the software interface might be different from the name in this guide, depending on the version of NVCS in use. With this setting turned on, instrument performance data are sent to Illumina. This data helps Illumina troubleshoot more easily and detect potential failures, enabling proactive maintenance and maximizing instrument uptime.
  • Page 27 ID, and the flow cell ID and the library ID must be specified in the file. The file name and values are not case-sensitive. External LIMS software can use the NovaSeq LIMS API to interact with the NovaSeq 6000. Contact Illumina Technical Support for more information on the API endpoints.
  • Page 28 "use_custom_read2_primer":false, "use_custom_index_read1_primer":false NovaSeq Standard and NovaSeq Xp Workflows The NovaSeq Standard and NovaSeq Xp workflows both use Illumina proprietary ExAmp chemistry. Standard Workflow The NovaSeq Standard workflow automates two crucial steps of Illumina proprietary ExAmp cluster chemistry onboard the instrument.
  • Page 29 NovaSeq 6000 Sequencing System Guide Onboard preparation and delivery of the Master Mix minimizes user interaction and reduces variability in the prepared mix. As part of the run setup for the Standard workflow, a library tube containing the denatured and neutralized library pool at recommended concentration is inserted into position #8 of the cluster cartridge.
  • Page 30 Select Save. Sample Sheet Name When running NovaSeq Control Software v1.3.1, or earlier, a sample sheet used for a NovaSeq 6000 run and uploaded to BaseSpace Sequence Hub must be named SampleSheet.csv (case-sensitive). If the sample sheet is incorrectly named and Run Monitoring and Storage is enabled, BaseSpace Sequence Hub flags the run for attention.
  • Page 31 Spiking in PhiX control. Consumables in Illumina Kits One NovaSeq 6000 Reagent Kit is needed to sequence one flow cell. Each kit is comprised of multiple consumables, which are listed in the following table. For a dual flow cell run, use two kits.
  • Page 32 NovaSeq 6000 Sequencing System Guide Table 9 Consumables in a NovaSeq 6000 Reagent Kit Consumable (One of Each) Purpose Buffer cartridge Provides sequencing buffers for the run. Cluster cartridge Provides clustering, indexing, and paired-end reagents for the run. Flow cell The clustering and sequencing reaction happens on the flow cell.
  • Page 33 NovaSeq 6000 Sequencing System Guide Equipment Item Source Freezer, -25°C to -15°C General lab supplier Ice bucket General lab supplier Pipette, single channel, 20 µl General lab supplier Pipette, single channel, 200 µl General lab supplier Pipette, single channel, 1000 µl General lab supplier Refrigerator, 2°C to 8°C...

  • Page 34: Chapter 4 Standard Workflow: Preparing Consumables

    NovaSeq 6000 Sequencing System Guide Chapter 4 Standard Workflow: Preparing Consumables Methods Library Guidelines Thaw SBS and Cluster Cartridges Empty Used Reagent Bottles Prepare Flow Cell Pool and Denature Libraries for Sequencing Methods Make sure that you have the required consumables and equipment. See...

  • Page 35: Empty Used Reagent Bottles

    NovaSeq 6000 Sequencing System Guide Place each cartridge into a wire thaw rack. The racks are provided with the instrument and prevent capsizing in the water bath. Figure 12 Cartridges in Wire Thaw Racks Thaw in a room temperature water bath (19°C to 25°C).
  • Page 36 Handle used reagents as chemical waste and discard in accordance with applicable regional, national, and local laws and regulations. For additional environmental, health, and safety information, see the SDS at support.illumina.com/sds.html. Remove and empty the small used reagent bottle as follows.

  • Page 37: Prepare Flow Cell

    NovaSeq 6000 Sequencing System Guide Prepare Flow Cell Remove a new flow cell package from 2°C to 8°C storage. Set the sealed flow cell package aside for 10-15 minutes to allow the flow cell to reach room temperature. Use the flow cell within 12 hours of removing it from the package.
  • Page 38 If you have optimized a final loading concentration for HiSeq™ X, HiSeq™ 4000, or HiSeq™ 3000, use 1.5× that concentration for NovaSeq 6000. For example, if your final loading concentration for HiSeq X is 200 pM, use 300 pM for NovaSeq 6000.
  • Page 39 NovaSeq 6000 Sequencing System Guide When spiking in PhiX, 1% is the recommended amount for well-balanced libraries. Low-diversity libraries can require more. To use a PhiX control with low-diversity libraries, contact Illumina Technical Support for guidance. Prepare a Fresh Dilution of NaOH Prepare a fresh dilution of 0.2 N NaOH to denature libraries for sequencing.
  • Page 40 NovaSeq 6000 Sequencing System Guide Transfer the full volume of denatured library or denatured library and PhiX to the library tube provided with the NovaSeq 6000 Reagent Kit. Immediately proceed to loading the library tube into the cluster cartridge and setting up the run.

  • Page 41: Chapter 5 Novaseq Xp Workflow: Preparing Consumables

    NovaSeq 6000 Sequencing System Guide Chapter 5 NovaSeq Xp Workflow: Preparing Consumables NovaSeq Xp Workflow Summary Methods Library Guidelines Thaw SBS and Cluster Cartridges Empty Used Reagent Bottles Prepare Flow Cell Pool, Denature, and Load Libraries for Sequencing NovaSeq Xp Workflow Summary NOTE Staggered start of new runs is only supported with the NovaSeq Standard workflow.

  • Page 42: Methods

    NovaSeq 6000 Sequencing System Guide 11 Load ExAmp/library mix onto the flow cell. 12 Load an empty library tube into position #8 of the cluster cartridge. Methods Make sure that you have the required consumables and equipment. See User-Supplied Consumables...

  • Page 43: Empty Used Reagent Bottles

    NovaSeq 6000 Sequencing System Guide Place each cartridge into a wire thaw rack. The racks are provided with the instrument and prevent capsizing in the water bath. Figure 15 Cartridges in Wire Thaw Racks Thaw in a room temperature water bath (19°C to 25°C).
  • Page 44 Handle used reagents as chemical waste and discard in accordance with applicable regional, national, and local laws and regulations. For additional environmental, health, and safety information, see the SDS at support.illumina.com/sds.html. Remove and empty the small used reagent bottle as follows.

  • Page 45: Prepare Flow Cell

    NovaSeq 6000 Sequencing System Guide Prepare Flow Cell Remove a new flow cell package from 2°C to 8°C storage. Set the sealed flow cell package aside for 10-15 minutes to allow the flow cell to reach room temperature. Use the flow cell within 12 hours of removing it from the package.
  • Page 46 The optimal DNA loading concentration depends on the library type and insert size. The following table provides DNA loading concentrations that are recommended based on Illumina libraries with insert sizes that are ≤ 450 bp. Load libraries with smaller insert sizes at the lower end of the recommended range. For libraries >...
  • Page 47 NovaSeq 6000 Sequencing System Guide NOTE Libraries might need to be titrated to obtain optimal seeding concentration. When the optimal loading concentration is determined, it is applicable for identical library types. Document # 1000000019358 v07 Material # 20023471 For Research Use Only. Not for use in diagnostic procedures.
  • Page 48 Nondenatured Library Pool (µl) When spiking in PhiX, 1% is the recommended amount for well-balanced libraries. Low-diversity libraries can require more. To use a PhiX control with low-diversity libraries, contact Illumina Technical Support for guidance. Prepare a Fresh Dilution of NaOH Prepare a fresh dilution of 0.2 N NaOH to denature libraries for sequencing.
  • Page 49 NovaSeq 6000 Sequencing System Guide Denature Library Pool and Optional PhiX Control Add 0.2 N NaOH to the tube of nondenatured library pool and optional PhiX as follows. Mode 0.2 N NaOH (µl) Nondenatured Library Pool (µl) Resulting Volume 18.0 22.0 µl, or 22.7 µl with PhiX 22.0...
  • Page 50 NovaSeq 6000 Sequencing System Guide Prepare the Flow Cell and Dock Place the NovaSeq Xp flow cell dock on a flat surface. Keep the flow cell level until it is loaded onto the instrument. Inspect the dock and make sure that it is free from particulate.
  • Page 51 NovaSeq 6000 Sequencing System Guide A NovaSeq Xp manifold wells facing up B NovaSeq Xp manifold arms placed in dock cutouts 12 Close the clamp to secure the flow cell and NovaSeq Xp manifold and seal the gaskets. 13 Discard the NovaSeq Xp manifold after loading library pools into the flow cell.
  • Page 52 NovaSeq 6000 Sequencing System Guide Prolonged incubation might reduce the percentage of clusters passing filter (%PF). Start the run within 30 minutes after loading library pools on the flow cell. Immediate use of the ExAmp/library mix yields best results. Add ExAmp Master Mix to each denatured library pool as follows, and then vortex for 20–30 seconds to mix.
  • Page 53 Gently tap the bottom of each cartridge on the bench to reduce air bubbles. Load Empty Library Tube Uncap the library tube provided with the NovaSeq 6000 Reagent Kit. Insert uncapped, empty library tube into the Library Tube position (#8) of the cluster cartridge.

  • Page 54: Chapter 6 Sequencing

    Chapter 6 Sequencing Set Up a Sequencing Run Monitor Run Progress Delete the Run Detach Position #30 Automatic Post-Run Wash Set Up a Sequencing Run Remove any items from the surface of the instrument. Keep the surface clear during the sequencing run and avoid leaning on the instrument. Pressure to the flow cell door can cause it to open, which stops the run.
  • Page 55 NovaSeq 6000 Sequencing System Guide If particulate is visible on either of the glass surfaces, clean the applicable surface with a lint-free alcohol wipe and dry with a low-lint lab tissue. Discard the package appropriately. NOTE Some scratches and other minor cosmetic defects on the flow cell are normal and do not affect data quality.
  • Page 56 The used buffer cartridge has pierced foil seals. Place a new buffer cartridge into the buffer drawer so that the Illumina label faces the front of the drawer. Align the cartridge with the raised guides on the drawer floor and sides.
  • Page 57 NovaSeq 6000 Sequencing System Guide Figure 25 Load the Buffer Cartridge If both used reagents bottles have been emptied, select the checkbox acknowledging that both used reagent bottles are empty. WARNING Failure to empty the used reagent bottles can result in a terminated run and overflow, which damages the instrument and poses a safety risk.
  • Page 58 NovaSeq 6000 Sequencing System Guide In the Run Name field, enter a name of your preference to identify the current run. The run name can contain alphanumeric characters, hyphens, and underscores. Enter the number of cycles for each read and index length in the sequencing run.

  • Page 59: Monitor Run Progress

    NovaSeq 6000 Sequencing System Guide NOTE To avoid overfilling the hard drive, do not copy any data to C:\ after the run starts. If pre-run checks fail, select Retry to restart the failed check or Retry All to restart all checks.

  • Page 60: Delete The Run

    While wearing gloves, push the white plastic tab labeled Detach after use to the right. Place a hand or solid surface under the reservoir and press the clear plastic tab toward the Illumina label to release the reservoir from under the cluster cartridge.

  • Page 61: Automatic Post-Run Wash

    NovaSeq 6000 Sequencing System Guide NOTE Avoid stacking cluster cartridges when storing. Stacking may cause accidental detachment of the reservoir. Figure 27 Removable Position #30 A White plastic tab to detach B Clear plastic tab to release Dispose of the reservoir in accordance with applicable standards.

  • Page 62: Chapter 7 Maintenance

    Software Updates Preventive Maintenance Illumina recommends that you schedule a preventive maintenance service each year. If you are not under a service contract, contact your Territory Account Manager or Illumina Technical Support to arrange for a billable preventive maintenance service.
  • Page 63 NovaSeq 6000 Sequencing System Guide Remove the lid from the center well of the SBS wash cartridge. Add wash solution to the center well. Fill to the fill line, which indicates the minimum required volume. The other reservoirs remain empty.
  • Page 64 NovaSeq 6000 Sequencing System Guide From the Home screen, select Wash, and then select which side to wash: A+B—Wash both sides simultaneously. A—Wash side A only. B—Wash side B only. The software initiates the series of wash screens. NOTE A maintenance wash for a single side can only be started when the other side is either idle or performing SBS read cycles.

  • Page 65: Staggered Start Of Runs On Flow Cell A And Flow Cell B

    NovaSeq 6000 Sequencing System Guide Return the small used reagent container to the alcove. Remove the large used reagent bottle and discard the contents in accordance with applicable standards. Return the large used reagent bottle to the buffer drawer. Put on a new pair of powder-free gloves.

  • Page 66: Software Updates

    The timer may display the Waiting... state until the cycle is complete. Software Updates NOTE The NovaSeq 6000 must be connected to the internet to check for software updates and to download updates. Software updates can be downloaded and installed from NVCS. Automatic checking for software updates is enabled by default.

  • Page 67: Appendix A Troubleshooting

    The support page provides access to documentation, downloads, and frequently asked questions. For access to support bulletins, sign in to your MyIllumina account. For run quality or performance problems, contact Illumina Technical Support. See Technical Assistance on page 79. To facilitate troubleshooting, consider sharing a link to the run summary in BaseSpace Sequence Hub with Illumina Technical Support.

  • Page 68: Process Management Troubleshooting

    During the pre-run check, sensors detect whether the leak tray contains any liquids: If the leak tray contains liquid but is not full, the run can proceed but you must contact Illumina Technical Support. See Technical Assistance on page If the leak tray is full, the run cannot proceed and you must contact Illumina Technical Support.

  • Page 69: End A Run

    You can let the maintenance wash complete instead of canceling it. End a Run Ending a run on the NovaSeq 6000 system is final . The software cannot resume the run or save sequencing data, and consumables cannot be reused.

  • Page 70: Shut Down The Instrument

    Wait at least 60 seconds before turning on the instrument again. CAUTION Do not relocate the instrument. Improper moving can affect optical alignment and compromise data integrity. For relocation assistance, contact your Illumina representative. Document # 1000000019358 v07Material # 20023471 For Research Use Only. Not for use in diagnostic procedures.

  • Page 71: Appendix B Real-Time Analysis

    Real-Time Analysis Workflow Real-Time Analysis Overview The NovaSeq 6000 Sequencing System runs RTA3, an implementation of Real-Time Analysis software, on the instrument Compute Engine (CE). RTA3 extracts intensities from images received from the camera, performs base calling, assigns a quality score to base calls, aligns to PhiX, and reports data in InterOp files for viewing in Sequencing Analysis Viewer.
  • Page 72 NovaSeq 6000 Sequencing System Guide Flow Cell Tiles Tiles are small imaging areas on the flow cell. The camera takes one image of each swath, which the software divides into tiles for RTA3 processing. The total number of tiles depends on how many lanes, swaths, and surfaces are imaged on the flow cell.

  • Page 73: Real-Time Analysis Workflow

    NovaSeq 6000 Sequencing System Guide Real-Time Analysis Workflow Registration Records the location of each cluster on the patterned flow cell. Intensity extraction Determines an intensity value for each cluster. Phasing correction Corrects the effects of phasing and prephasing. Base calling Determines a base call for every cluster.
  • Page 74 NovaSeq 6000 Sequencing System Guide Base Calling Base calling determines a base (A, C, G, or T) for every cluster of a given tile at a specific cycle. The NovaSeq 6000 Sequencing System uses two-channel sequencing, which requires only two images to encode the data for four DNA bases, one from the red channel and one from the green channel.
  • Page 75 NovaSeq 6000 Sequencing System Guide Q-Score Q(X) Error Probability 0.0001 (1 in 10,000) 0.001 (1 in 1000) 0.01 (1 in 100) 0.1 (1 in 10) Quality Scoring and Reporting Quality scoring calculates a set of predictors for each base call, and then uses the predictor values to look up the Q-score in a quality table.

  • Page 76: Appendix C Output Folders And Files

    Appendix C Output Folders and Files Sequencing Output Folder Structure Sequencing Output Files Sequencing Output Folder Structure The control software generates the output folder name automatically. Config—Configuration settings for the run. Logs—Log files describing operational steps, instrument analytics, and RTA3 events. Data Intensities BaseCalls...

  • Page 77: Sequencing Output Files

    NovaSeq 6000 Sequencing System Guide Sequencing Output Files File Type File Description, Location, and Name Base call files Each cluster analyzed is included in a base call file, aggregated in one file per cycle, lane, and surface. The aggregated file contains the base call and encoded quality score for every cluster.

  • Page 78: Appendix D Windows Security

    CAUTION Because these configurations affect system performance and can compromise security, contact Illumina Technical Support when it is unclear whether a setting needs editing or the impact is unknown.

  • Page 79: Software Restriction Policies

    Windows Software Restriction Policies (SRP) use rules to allow only specified software to run. For the NovaSeq 6000, SRP rules are based on certificates, file names and extensions, or directories. By default, SRP is turned on to prevent unwanted software from running on the control computer. An IT representative or system administrator can add and remove rules to customize the security level.
  • Page 80 NovaSeq 6000 Sequencing System Guide Directories C:\LocalSymbols\* C:\Program Files (x86)\Chromium\Application\* C:\Program Files (x86)\EMET 5.5\* C:\Program Files (x86)\Illumina\* C:\Program Files (x86)\Internet Explorer\* C:\Program Files (x86)\LibreOffice 5\* C:\Program Files\Illumina\* C:\ProgramData\Illumina\* C:\ProgramData\Package Cache\* C:\Users\sbsuser\AppData\Local\Temp\Citrix\* C:\Users\sbsuser\AppData\Local\Temp\CitrixLogs\* C:\Users\sbsuser\Desktop\FSE turn over to customer.bat D:\Illumina\* Add and Remove SRP Rules Add and remove SRP rules to customize system security.
  • Page 81 NovaSeq 6000 Sequencing System Guide Immediately turn SRP back on: Navigate to the directory C:\Illumina\Security. b Double-click Enable.reg. 10 If SRP rules were modified for the first time, log off and then log on again for the rules to take effect.

  • Page 82: Index

    Index compartments 5 Compute Engine 8, 53, 64 %PF 27, 35, 67 consumables diluting and denaturing 23 laboratory-grade water 25 maintenance washes 55 packaging 16 administrator account 73 unloading 53-54, 58 alignment failure 60 control computer 71 amplification 2 control software 7 analysis 23 cross-contamination 7, 54 analysis methods 2...
  • Page 83 NovaSeq 6000 Sequencing System Guide expiration dates 16 imaging 2, 12, 64-65 inbound connections 71 Index Reads 51 individually addressable lanes 3, 15 initialization 18 FASTQ conversion 23, 64 input wells 15 files insert sizes 31, 39 run-specific 60 instrument performance data 19...
  • Page 84 NovaSeq 6000 Sequencing System Guide preventive maintenance 55 privileges 73 Process Management 53 nanowells 66 NaOCl 54-55 no calls 66-67 normalization 30, 38 Q-scores 52, 67-68 NovaSeq Xp dock 43, 47 quality control 27, 35 NovaSeq Xp manifold wells, numbering 15...
  • Page 85 NovaSeq 6000 Sequencing System Guide saving reagent cartridges 61 two-lane flow cells 12 scanning 2 scratches, flow cells 43, 47 security 72 customizing 73 Universal Copy Service 7-8, 53 security settings 71 unloading reagent cartridges 49 sensors 5, 57, 60...

  • Page 86: Technical Assistance

    Other countries +44.1799.534000 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. Document # 1000000019358 v07Material # 20023471...

  • Page 87: Document # 1000000019358 V07 Material # 20023471

    Document # 1000000019358 v07 Material # 20023471 Illumina 5200 Illumina Way San Diego, California 92122 U.S.A. +1.800.809.ILMN (4566) +1.858.202.4566 (outside North America) techsupport@illumina.com www.illumina.com For Research Use Only. Not for use in diagnostic procedures. © 2018 Illumina, Inc. All rights reserved.

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