⚠️ The configuration provided in this integration has been established to support NovaSeq X Series lab processes. Any configuration changes to protocols or workflows (including renaming protocols, steps, and fields) could break the process.
Prerequisites and Assumptions
⚠️ The NovaSeq X Series Integration v1.2.0 requires a valid BaseSpace Sequence Hub account with an Enterprise or Professional subscription.
Analysis Configuration Template
The NovaSeq X Series Sequencing v1.1 workflow uses analysis configuration templates (ACTs) to configure secondary analysis for planned runs. Required ACTs must be created using BaseSpace Sequence Hub. The ACT names must be unique. The index adapter kit (the label group in Clarity LIMS) selected in the ACT is created in Clarity LIMS. The same label group must be used in the library preparation step. For more information, refer to NovaSeq X Series Integration v1.2.0 User Interaction, Validation and Troubleshooting.
⚠️ Make sure that ACT names created in BaseSpace Sequence Hub do not have leading or trailing spaces. Otherwise, Clarity LIMS can have issues with recognizing the ACT names.
Samples
Samples must go through the library preparation and quantification process before they enter the NovaSeq X Series Sequencing v1.1 workflow. It is assumed that the following steps have completed before samples are assigned to the workflow:
Samples have been accessioned into Clarity LIMS.
Samples have been run through QC and library prep.
Samples have the Molarity (nM) global field set to a value.
This value is required for the Calculate Volumes automation in the Make Bulk Pool step.
⚠️ Sample and library names must use only alphanumeric, dash, or underscore characters.
The NovaSeq X Series Integration Package v1.2 includes the following workflows:
NovaSeq X Series Sequencing v1.1
Library Prep Validation v2.3.2 (optional, but recommended for validation purposes)
The following describes the protocols and steps included in these workflows.
Library Prep Validation v2.3.2 Workflow
Protocol 1: Library Prep Validation v2.3.2
Purpose:
Included for validation purposes only, this protocol models the library prep steps required to advance samples to the NovaSeq X Series Sequencing v1.1 workflow.
The protocol contains a single step - Library Prep Validation v2.3.2. After this step, a routing script sends the samples to the first step of the NovaSeq X Series Sequencing v1.1 workflow (Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.1)).
Steps:
Library Prep Validation v2.3.2
NovaSeq X Series Sequencing v1.1 Workflow
Protocol 1: NovaSeq X Series Sequencing v1.1
Purpose:
This protocol models the lab processes of run setup for starting a NovaSeq X Series sequencing and secondary analysis run.
Steps:
Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.1)
The secondary analysis of samples is configured using the ACT.
The labels applied to the samples are validated against the selected ACT so that samples use valid labels.
Make Bulk Pool (NovaSeq X Series Sequencing v1.1)
The Calculate Volume script assists with pooling samples and adding resuspension buffers and reagents.
The Validate Analysis Configurations automation validates the ACT of pooled samples to make sure that the secondary analysis configurations remain valid after pooling.
Dilute and Denature (NovaSeq X Series Sequencing v1.1)
The Calculate Volume script helps denature and dilute samples from step 2 to the final loading concentration.
Load To Library Tube Strip (NovaSeq X Series Sequencing v1.1)
The library pools from step 3 are ready to be loaded to the NovaSeq X Series library tube strip.
Validates run and analysis information.
Generates the sample sheet and creates the planned run, depending on the run mode.
AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.1)
The step is fully automated and starts and completes automatically after the sequencing run is started and completed on the instrument side.
The sequencing run metadata (eg, run configuration, primary run metrics, and so on) are recorded automatically.
⚠️ Do not add samples to the Ice Bucket or start or complete the step. The integration does this automatically.
AUTOMATED - Analysis Run (NovaSeq X Series Sequencing v1.1)
The step is fully automated and starts and completes automatically after the analysis run is started and completed in ICA.
The analysis run metadata (eg, status and high level analysis summary) are recorded automatically.
⚠️ Do not add samples to the Ice Bucket or start or complete the step. The integration does this automatically.
Configure a custom library preparation workflow as follows.
Select Configuration, then select Lab Work.
Add a Routing Script automation to the last Master Step of the library preparation workflow.
Select Configuration, then select Automation.
Create a new Routing Script automation and update it as follows.
For Channel Name, enter limsserver.
For Command Line, enter the following script:
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeq X Series' \
--WORKFLOW 'NovaSeq X Series v1.1' \
--STEP 'Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
For Automation Use, select the custom library preparation workflow.
Step 1: Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.1)
The Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.1) step uses ACTs to configure secondary analysis for samples. Each ACT contains details related to the secondary analysis (e.g., index adapter kit to use, reference genome setting, and so on). You can select an ACT from a list and assign samples to it. A planned run can have multiple ACTs and this step must be repeated for each ACT that is required for the run. For more information on creating ACTs and assigning samples to them, refer to NovaSeq X Series Integration v1.2.0 User Interaction, Validation and Troubleshooting.
Validate Sample Names and Retrieve Analysis Configuration Template List and Register Step Started Automation¹
Automatically triggered on entry to the step, this automation completes the following actions:
Checks that submitted sample names contain only alphanumeric, dash, and underscore characters.
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -exp 'submittedSamples.each { sample -> if ( !sample.name.matches( ::[A-Za-z0-9_-]+:: ) ) { fail ( ::Submitted sample :: + sample.name + :: should only have alphanumeric, dash, and underscore characters. Please rename and try again.:: ) } }' -log {compoundOutputFileLuid1}
Retrieves the list of ACTs that were created in BaseSpace Sequence Hub.
¹ These automations are required for the NovaSeq X Series Sequencing v1.1 workflows and contain additional logic needed for CLPA support. If you would like to remove support for CLPA, contact Illumina Support.
² These automations are required for CLPA support only.
All remaining automations are required for the NovaSeq X Series Sequencing v1.1 workflows.
Master Step Fields
The following table lists the configuration details for fields that are defined on the Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.1) step.
Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.1) Master Step Field Configuration
Field Name
Field Type
Options
Analysis Configuration Template
Text Dropdown
Required Field
Application
Text
Read Only
Application Version
Text
Read Only
Index Adapter Kit
Text
Read Only
Library Prep Kit
Text
Read Only
Reference Genome
Text
Read Only
Secondary Analysis Mode
Text
Read Only
Global Fields
The following table lists the global custom fields that are configured to display on the Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.1) step.
Global Field Configuration (Derived Sample)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Molarity (nM)
Numeric
Decimal places displayed = 2
ACT Name
Text
Read Only
Step 2: Make Bulk Pool (NovaSeq X Series Sequencing v1.1)
Samples are pooled in the Make Bulk Pool (NovaSeq X Series Sequencing v1.1) step. You can manually create working pools based on the final loading concentration required.
Register Step Started Automation¹
Automatically triggered on entry to the step, this automation registers the start time of the step. This automation completes this action by publishing messages to CLPA through ICA.
Automatically triggered on exit of the Pooling screen, this automation performs analysis configuration validity and checks each pool for the following characteristics:
Pooled samples are within the maximum configuration limit.
Pooled samples have the same type of analysis (e.g., Cloud or Local).
Pooled samples that have the same secondary analysis also have the same analysis version (e.g., v3.8.4) and analysis settings (e.g., Map/Align Output Format = CRAM).
Automatically triggered when you select Calculate Volumes on the Record Details screen, this automation completes the following actions:
Proceeds if the sample has molarity values.
if (!input.hasValue(::Molarity (nM)::)) { return; };
Uses Number of Samples in Pool to calculate the volumes needed for the 2 nM intermediate library pools.
if (output.hasValue(::Number of Samples in Pool::)) { output.::Number of Samples in Pool:: = output.::Number of Samples in Pool:: + 1; } else { output.::Number of Samples in Pool:: = 1; }' -t true
Uses the Bulk Pool Volume (ul) field and Number of Lanes to Sequence (x100) to calculate volumes needed for the 2 nM intermediate library pools.
Copies the Final Loading Concentration (pM) and Flowcell Type from the step inputs to the step outputs.
output.::Bulk Pool Volume (ul):: = 100 * step.::Number of Lanes to Sequence::; output.::NovaSeq X Flowcell Type:: = step.::Flowcell Type::; output.::Final Loading Concentration (pM):: = step.::Final Loading Concentration (pM)::;
Calculates the per sample volume required for each library to make a 2 nM intermediate library pool and sets the total sample volume to zero.
input.::Per Sample Volume (ul):: = 2 * output.::Bulk Pool Volume (ul):: / input.::Molarity (nM):: / output.::Number of Samples in Pool::;output.::Total Sample Volume (ul):: = 0;' -t true
Calculates the adjusted per sample volume for the pools.
Uses the Total Sample Volume (ul) to calculate the RSB volume (ul) required to top up the pools that are needed to create the 2 nM intermediate library pools. The RSB volume is saved to the file in the Calculation File placeholder in the Files section.
Uses the NovaSeqXSeries_Bulk_Pool1.csv and NovaSeqXSeries_Bulk_Pool2.csv template files to generate a single CSV file. This file contains information about the pools and the samples that they contain. The generated file is stored in the Calculation File placeholder in the Files section.
Automatically triggered on exit of the step, this automation completes the following actions:
Registers the pool and library information used by the Clarity LIMS workflow. Samples in the pool are assumed to have gone through library preparation.
This automation completes this action by publishing messages to CLPA through ICA.
¹These automations are required for CLPA support only.
All remaining automations are required for the NovaSeq X Series Sequencing v1.1 workflows.
Master Step Fields
The following table lists configuration details for the fields that are defined on the Make Bulk Pool (NovaSeq X Series Sequencing v1.1) step.
Make Bulk Pool (NovaSeq X Series Sequencing v1.1) Master Step Field Configuration
Field Name
Field Type
Options
Additional Options and Dropdown Items
Final Loading Concentration (pM)
Numeric Dropdown
Required Field
Custom Entries
Dropdown Items
90
140
150
160
180
Range from 0
Decimal places displayed: 0
Flowcell Type
Text
Required Field
Dropdown Items
1.5B
10B
25B
Minimum Per Sample Volume (ul)
Numeric
Required Field
Decimal places displayed: 2
Default: 2
Number of Lanes to Sequence
Numeric
Required Field
Range: 1–10
Decimal places displayed: 0
Global Fields
The following table lists the global custom fields that are configured to display on the Make Bulk Pool (NovaSeq X Series Sequencing v1.1) step.
Global Custom Fields Configuration (Derived Sample)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Final Loading Concentration (pM)
Numeric Dropdown
Required Field
Custom Entries
Decimal places displayed: 0
Dropdown Items
225
400
RSB Volume (ul)
Numeric
Read Only
Decimal places displayed: 2
NovaSeq X Flowcell Type
Text Dropdown
Required Field
Read Only
Dropdown Items
1.5B
10B
25B
Step 3: Dilute and Denature (NovaSeq X Series Sequencing v1.1)
The Dilute and Denature (NovaSeq X Series Sequencing v1.1) step allows you to dilute pooled samples with the addition of RSB.
Validate Inputs Flowcell Type and Register Step Started¹
Automatically triggered on entry to the step, this automation completes the following actions:
Checks that the specified flow cell type is valid.
⚠️ This script is required for the NovaSeq X Series Sequencing v1.1 workflow to function properly.
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -h false -exp 'if (!input.hasValue(::NovaSeq X Flowcell Type::)){fail(::Invalid Flowcell Type custom field value. Please make sure all input samples have a value assigned for Flowcell Type custom field.::)}' -log {compoundOutputFileLuid1}
Registers the start time of the step by publishing messages to CLPA through ICA.
Automatically triggered when you select Calculate Volumes on the Record Details screen, this automation completes the following actions based on the NovaSeq X Flowcell Type selected:
Sets the NaOH Volume (µl) and TT2 Volume (µl) field values.
Computes the BP Aliquot Volume (µl) and RSB Volume (µl) required for the dilution of pools to the required final loading concentration.
ℹ️ The BP Aliquot Volume value is rounded up to the nearest µl. The value in the calculation file, however, is reflected with up to two decimal places.
Sets the PhiX Volume (µl) and PhiX Concentration (µl) if there is a PhiX spike-in.
Generates a single CSV file that contains information about the reagents volume required to dilute the working pools. The generated file is stored in the Calculation File placeholder in the Files section.
¹ These automations are required for the NovaSeq X Series Sequencing v1.1 workflows and contain additional logic needed for CLPA support. If you would like to remove support for CLPA, contact Illumina Support.
² These automations are required for CLPA support only.
All remaining automations are required for the NovaSeq X Series Sequencing v1.1 workflows.
Global Fields
The following table lists the global custom fields that are configured to display on the Dilute and Denature (NovaSeq X Series Sequencing v1.1) step.
Global Field Configuration (Derived Sample)
Field Name
Field Type
Options
Additional Options and Dropdown Items
BP Aliquot Volume (ul)
Numeric
Read Only
Decimal places displayed = 0
NaOH Volume (ul)
Numeric
Read Only
Decimal places displayed = 2
RSB Volume (ul)
Numeric
Read Only
Decimal places displayed = 2
TT2 Volume (ul)
Numeric
Read Only
Decimal places displayed = 2
Step 4: Load to Library Tube Strip (NovaSeq X Series Sequencing v1.1)
The Load to Library Tube Strip (NovaSeq X Series Sequencing v1.1) step allows you to scan the library tube strip barcode into Clarity LIMS. Then, you can place the working pools into the library tube strip used in the NovaSeq X Series run. This step also does the following actions:
Validates the run setup and analysis information.
Generates the sample sheet file.
Creates a planned run on Illumina Connected Analytics (ICA), depending on the selected run mode.
Validate Flowcell Inputs and Validate Analysis Configurations and Register Step Started Automation¹
Automatically triggered on entry to the step, this automation completes the following actions:
Checks that the selected destination container types on the Load to Library Tube Strip step matches the selected flow cell type of the samples. The 1.5B flow cell is compatible with the library 2-tube strip and the 10B and 25B flow cells are compatible with the library 8-tube strip.
Performs basic checks on the secondary analysis configuration of the samples in the same planned run. The following checks are included in this script:
Secondary analysis configuration of samples in a planned run is within maximum configuration limit.
Samples in a planned run have the same type of analysis (e.g., Cloud or Local).
Samples in the same pools that have the same secondary analysis (e.g., Illumina DRAGEN Enrichment) also have the same analysis settings (e.g., Map/Align Output Format = CRAM) and the same analysis version (e.g., v3.8.4).
⚠️ This script is required for the NovaSeq X Series Sequencing v1.1 workflow to function properly.
Automatically triggered on the Placement screen, this automation validates the library tube strip barcode to make sure that it conforms to the barcode mask LC[0-9]{7}-LC1 for the library 8-tube strip and LC[0-9]{7}-L[A-Z]2 for the library 2-tube strip.
Validate Run Setup and Create Planned Run Automation
Automatically triggered after a selection on the Record Details screen, this automation completes the following actions:
Validates the parameters entered on the Record Details screen. These parameters are used to set up the run, generate the sample sheet file, and create the planned run in ICA, depending on the run mode.
Run Name can only contain alphanumeric, dash, underscore, or period characters. Do not use spaces.
if (!step.::Run Name::.matches(::[a-zA-Z0-9-_]+[a-zA-Z0-9-_. ]*::)) { fail(::Run Name contains prohibited characters. Please check to make sure Run Name only contains alphanumeric characters, spaces, dashes and underscores. Run Name must start with alphanumeric, a dash or an underscore::);}
Run Name cannot exceed 255 characters.
if (step.::Run Name::.length() > 255) { fail(::Run Name shall not exceed 255 characters.::); };
Checks the Index 1 Cycles and Index 2 Cycles field values. If Index 2 Cycles is greater than 0, the Index 1 Cycles value must be greater than 0 or an error can occur.
if (step.::Index 2 Cycles:: > 0 && step.::Index 1 Cycles:: == 0) { fail(::Index 1 Cycles cannot be zero if Index 2 Cycles is non-zero::); };
Generates the sample sheet and creates the planned run in ICA. The sample sheet is attached to the step.
There is a backend validation of the sample sheet content in ICA. This validation makes sure that the sample sheet is valid to set up a Local mode run and that it is ready for use with DRAGEN applications.
¹ These automations are required for the NovaSeq X Series Sequencing v1.0 workflows and contain additional logic needed for CLPA support. If you would like to remove support for CLPA, contact Illumina Support.
² These automations are required for CLPA support only.
All remaining automations are required for the NovaSeq X Series Sequencing v1.0 workflows.
Master Step Fields
The following table shows the master step fields that are configured on the Load to Library Tube Strip (NovaSeq X Series Sequencing v1.1) step. These fields are required for sample sheet generation and planned run creation in ICA.
Load to Library Tube Strip (NovaSeq X Series Sequencing v1.1) Master Step Field Configuration
Field Name
Field Type
Options
Additional Options and Dropdown Items
Cloud Run ID
Text
Read Only
Hidden
ℹ️ Used for creating a planned run in ICA.
Index 1 Cycles
Numeric Dropdown
Required Field
Custom Entries
Range = 0–20
Presets
0
6
8
Index 2 Cycles
Numeric Dropdown
Required Field
Custom Entries
Range = 0–20
Presets
0
6
8
Read 1 Cycles
Numeric Dropdown
Required Field
Custom Entries
Range = 1–251
Presets
51
101
151
Read 2 Cycles
Numeric Dropdown
Required Field
Custom Entries
Range = 0–251
Presets
51
101
151
Run Mode
Text Dropdown
Required Field
Presets
Local
Cloud
Run Name
Text
Required Field
Step 5: AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.1)
The AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.1) step is fully automated. The integration starts the step, adds samples to the Ice Bucket, and completes the step. Data from the run is parsed back to Clarity LIMS. In this step, pooled samples in the library tube strip are sequenced on the NovaSeq X Series instrument.
⚠️ Do not add samples to the Ice Bucket or start and complete the AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.1) step. The integration does this automatically.
Register Step Started & Register NovaSeq X Run & Register NovaSeq X Run Association & Register NovaSeq X RunStarted Automation¹
Automatically triggered at the beginning of the step, this automation completes the following actions:
Registers the start time of the step.
Registers the NovaSeq X Series sequencing run configuration.
Registers the association of the sequencing run with the samples by linking the Instrument Run ID with the sample ID.
Registers the time that the sequencing run started.
This automation completes these actions by publishing messages to CLPA through ICA.
Register NovaSeq X RunCompleted & Register Step Completed Automation¹
Automatically triggered on exit of the step, this automation completes the following actions:
Registers the sequencing run completion time, run status, and run metrics. This script requires the Cloud Run ID custom field from the Load to Library Tube Strip (NovaSeq X Series Sequencing v1.1) step.
Registers the completion time of the step.
This automation completes these actions by publishing messages to CLPA through ICA.
¹ These automations are required for CLPA support only.
Master Step Fields
The following tables show the master step fields that are configured on the AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.1) step.
Clarity LIMS Master Step Field Information
Field Name
Source File
Corresponding Field in Source File
Additional Information
Current Cycle
RunCompletionStatus.xml
CompletedReads
Visible on Record Details screen.
Calculated based on the CompletedReads field.
Current Read
RunCompletionStatus.xml
RunParameters.xml
CompletedReads
PlannedReads
Visible on Record Details screen.
Calculated based on the CompletedReads field in RunCompletionStatus.xml and PlannedReads field in RunParameters.xml.
Flow Cell Expiration Date
RunParameters.xml
ExpirationDate
Visible on Record Details screen.
Corresponds to the value in the ExpirationDate field under the ConsumableInfo field for FlowCell Type.
Flow Cell ID
RunParameters.xml
SerialNumber
Visible on Record Details screen.
Corresponds to the value in the SerialNumber field under the ConsumableInfo field for FlowCell Type.
Flow Cell Lot Number
RunParameters.xml
LotNumber
Visible on Record Details screen.
Corresponds to the value in the LotNumber field under the ConsumableInfo field for FlowCell Type.
Flow Cell Part Number
RunParameters.xml
PartNumber
Visible on Record Details screen.
Corresponds to the value of the PartNumber field under the ConsumableInfo field for FlowCell Type.
Flow Cell Side
RunParameters.xml
Side
Visible on Record Details screen.
Flow Cell Type
RunParameters.xml
FlowCellType
Visible on Record Details screen.
Instrument Control Software Version
RunParameters.xml
SystemSuiteVersion
Visible on Record Details screen.
Instrument ID
RunParameters.xml
InstrumentSerialNumber
Visible on Record Details screen.
Instrument Type
RunParameters.xml
InstrumentType
Visible on Record Details screen.
Output Folder
RunParameters.xml
OutputFolder
Visible on Record Details screen.
Library Tube Strip Barcode
RunParameters.xml
SerialNumber
Visible on Record Details screen.
Corresponds to the value of the SerialNumber field under the ConsumableInfo field for SampleTube Type.
Library Tube Lot Number
RunParameters.xml
LotNumber
Hidden
Corresponds to the value of the LotNumber field under the ConsumableInfo field for SampleTube Type.
Run End Time
RunCompletionStatus.xml
RunEndTime
Hidden
Run Name
RunParameters.xml
ExperimentName
Visible on Record Details screen.
RTA Version
Not used
Not used
Hidden
Other Clarity LIMS Master Step Fields
Field Name
Description
Additional Information
Run Status
Presets
RunStarted
RunCompletedSuccessfully
RunAbortedByUser
RunErroredOut
Set by the integration service.
Visible on Record Details screen.
Sequencing Log
Set by the integration service during the sequencing run.
Visible on Record Details screen.
BaseSpace Run ID
Received from the message sent to the integration service.
Hidden
ICA Project ID
Received from the message sent to the integration service.
Hidden
Instrument Run ID
Received from the message sent to the integration service.
Hidden
Run Start Time
Received from the message sent to the integration service.
Hidden
Global Fields
The following global custom fields are used to capture the run metrics in Clarity LIMS:
% Bases >=Q30 R1
% Bases >=Q30 R2
% Error Rate R1
% Error Rate R2
Yield (Gb) R1
Yield (Gb) R2
Reads PF R1
Reads PF R2
%PF R1
%PF R2
% Aligned R1
% Aligned R2
% Phasing R1
% Phasing R2
% Prephasing R1
% Prephasing R2
Intensity Cycle 1 R1
Intensity Cycle 1 R2
Cluster Density R1
Cluster Density R2
At the end of the step, the pools of samples are automatically removed from the step. The step completes automatically when Run Status is RunCompletedSuccessfully.
Step 6: AUTOMATED - Analysis Run (NovaSeq X Series Sequencing v1.1)
The AUTOMATED - Analysis Run (NovaSeq X Series Sequencing v1.1) step is fully automated. The integration starts and completes the step automatically. Data from the analysis is parsed back to Clarity LIMS. In this step, the secondary analysis configured using the Analysis Configuration Template (ACT) is performed in Illumina Connected Analytics (ICA). There are no automations associated with this step.
⚠️ Do not add samples to the Ice Bucket or start and complete the AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.1) step. The integration does this automatically.
Master Step Fields
The following tables show the master step fields that are configured on the AUTOMATED - Analysis Run (NovaSeq X Series Sequencing v1.1) step.
⚠️ Do not modify the names of the master step fields. Modifications cause the integration to break.
AUTOMATED - Analysis Run (NovaSeq X Series Sequencing v1.1) Master Step Field Information
Field Name
Description
Additional Information
Analysis Status
Presets
Started
Completed
Failed
NeedsAttention
Stopped
TimedOut
CompletedWithErrors
Set by the integration service.
Visible on Record Details screen.
Analysis Result Location
Received from the message sent to the integration service.
Visible on Record Details screen.
Library Tube Strip Barcode
Identified by the integration service using information from RunParameters.xml.
Hidden
How the Integration Works
The following information summarizes how the NovaSeq X Series integration works.
After the Validate Run Setup and Create Planned Run automation is triggered on the Load to Library Tube Strip (NovaSeq X Series Sequencing v1.1) step, the run parameters entered in the Run Details screen are sent to Illumina Connected Analytics (ICA). The analysis configuration parameters from the selected ACTs are also sent to ICA. ICA validates the run and analysis configuration. If the validation fails, ICA sends an error message to Clarity LIMS. If the validation passes, ICA generates the sample sheet and sends it back to Clarity LIMS. ICA also creates the planned run based on the selected run mode (e.g., Local or Cloud).
For the Local run mode, the sample sheet is generated and stored in Clarity LIMS. This sample sheet contains the run and analysis configuration information required to start the run on the NovaSeq X Series instrument.
For the Cloud run mode, the planned run is created in ICA. The planned run contains the run and analysis configuration information required to start the run on the instrument. The sample sheet is generated and stored in Clarity LIMS for reference purposes.
When the sequencing run starts on the instrument, the NovaSeq X Series Control Software notifies BaseSpace Sequence Hub. BaseSpace Sequence Hub monitors the run and notifies Clarity LIMS via the integration service. The events are processed and the integration service retrieves the run information from BaseSpace Sequence Hub. This information is used to populate the custom fields in the AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.1) step.
Other run events follow the same information flow. When sequencing is complete, the control software uploads the sequencing run data (primary metrics) and associated files to ICA. Then, Clarity LIMS retrieves the primary metrics and uses them to populate the fields in the Sample Details table (e.g., % Error Rate R1). The custom fields (e.g., Run Status, Current Read, and so on) on the AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.1) step are updated using the run related information. If the sequencing run is successfully completed, the step automatically completes.
The integration tracks the analysis events and results in the AUTOMATED - Analysis Run (NovaSeq X Series Sequencing v1.1) step. You must log in to BaseSpace Sequence Hub to retrieve the cloud analysis results. For local analysis, the secondary analysis results are in the external storage configured in Illumina Run Manager. The external storage information is found in the External Storage for Analysis Results configuration settings in Illumina Run Manager.
⚠️ If a planned run with the same sample name and project name (case-insensitive) has been created previously in ICA, the sample sheet generated from the Validate Run Setup and Create Planned Run automation can reflect the original case of the previous sample name. This can cause validation errors for analysis configurations with sample-level settings. To resolve this issue, change the sample name or the project name on Clarity LIMS and run the automation again.
Start a Sequencing Run on NovaSeq X Series Instrument
The following sections outline the steps to start a Clarity LIMS cloud or local run on the NovaSeq X Series instrument.
Run Mode Configuration
In the NovaSeq X Series Control Software, log in to the instrument using an account that has permissions for configuring settings.
On the menu, select Settings, then select Cloud settings.
In Run Settings, select the Cloud run storage checkbox.
For Hosting location, select the applicable location from the drop-down options.
[Optional] For Private domain name, enter the domain name according to the workgroup that was configured with the NovaSeq X Series integration package.
Select Save.
Start a Sequencing Run in Local Run or Cloud Run Modes
Start a Sequencing Run in Local Run Mode
Log in with the BaseSpace Sequence Hub account and select the workgroup used during the NovaSeq X Series integration package installation.
Import the sample sheet created in the Load to Library Tube Strip (NovaSeq X Series Sequencing v1.1) step. Refer to information on creating a local run in the NovaSeq X Plus Product Documentation on the NovaSeq X Plus Sequencing System support site.
When the sample sheet is selected, the contents are validated. After the validation passes, select Next.
Select Save As Planned.
Run and analysis data is parsed and auto-populates in the list of runs. For more information on planning a NovaSeq X Series run, refer to the Plan a NovaSeq X Series Run section of the BaseSpace Sequence Hub Online Help at help.basespace.illumina.com and the NovaSeq X Plus Product Documentation on the NovaSeq X Plus Sequencing System support site.
To start a sequencing run in cloud run mode, refer to information on starting a planned run in the NovaSeq X Plus Product Documentation on the NovaSeq X Plus Sequencing System support site.
Enabling Planned Run Generation for Samples Having Duplicate Name with Different Indexes
The following sections describe the components (files, properties, reagent categories / label groups, reagent kits, and containers) that are installed by default as part of this integration.
Reagent Kits
Buffer Cartridge
Lyophilization Cartridge
NaOH
Reagent Cartridge
Resuspension Buffer (RSB)
TT2
Container Types
Library 2-Tube Strip
Library 8-Tube Strip
Tube
This integration supports the library 8-tube strip with the barcode in the LC[0-9]{7}-L[A-Z]1 format. The integration also supports the library 2-tube strip with the barcode in the LC[0-9]{7}-L[A-Z]2 format.
Control Types
PhiX v3
Rules and Constraints
The workflow configuration contains several validation checks. To make sure that the calculations work properly, it is important that you do not disable any of this validation logic. The validation checks determine the following information:
Which samples, and how many, can enter each step together.
Which samples, and how many, can be pooled together.
All submitted samples must have an associated secondary analysis that is configured using the analysis configuration template (ACT). The ACT must be configured on BaseSpace Sequence Hub before starting the Assign Analysis Configuration Template step. The ACT names must be unique.
The library tube strip barcode must be unique. There must not be multiple library tube strip containers with the same name in the system.
Reagent labels, or indexes, must be unique.
One library pool can only contain one library or control with no label/index.
The AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.1) and AUTOMATED - Analysis Run (NovaSeq X Series Sequencing v1.1) steps must not be manually started or completed. These steps are fully automated and the sequencing service does not update samples correctly if they have been manually started.
For the automated run to start successfully, you must select Validate Run Setup and Create Planned Run in the Load to Library Tube step.
