Configuration
The Illumina NextSeq 1000/2000 Integration Package v2.5.0 supports the integration of Clarity LIMS to Illumina NextSeq 1000/2000 sequencing systems.
For instructions on validating and troubleshooting the NextSeq 1000/2000 Integration, refer to NextSeq 1000/2000 Integration v2.5.0 User Interaction, Validation and Troubleshooting.
⚠️ The configuration provided in this integration has been established to support NextSeq 1000/2000 lab processes. Any configuration changes to protocols or workflows — including renaming protocols, steps, and fields — could break the process.
Prerequisites and Assumptions
The Illumina NextSeq 1000/2000 Integration Package v2.5.0 is compatible with Illumina cloud hosted deployments only.
⚠️ This integration requires a Personal, Professional, or Enterprise BaseSpace Sequence Hub subscription.
It is assumed that samples entering the NextSeq 1000/2000 Sequencing v2.4 workflow have gone through library preparation and quantification processes. Before they are assigned to the workflow, samples have completed the following actions:
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 some value. The Calculate Volumes automation in the Library Pooling and Dilution step requires a value in the Molarity (nM) global field.
For more information on sample accessioning, refer to Sample Accessioning and Upload and Modify Samples in the Getting Started section of the Clarity LIMS (Clarity & LabLink Reference Guide) documentation.
You can assign samples to workflows automatically, using a routing script, or manually—from the Projects & Samples dashboard. Refer to Assign and Process Samples in the Clarity LIMS (Clarity & LabLink Reference Guide) documentation.
Workflows, Protocols, and Steps
The NextSeq 1000/2000 Integration Package v2.5.0 includes the following workflows:
NextSeq 1000/2000 Sequencing v2.4
[Optional] Library Prep Validation v2.3.3 (recommended for validation purposes)
The following protocols and steps are included in these workflows.
Library Prep Validation v2.3.3 Workflow
NextSeq 1000/2000 Sequencing v2.4 Workflow
Validation Workflow
The Library Prep Validation v2.3.3 workflow allows for validation of the system after installation is complete. For details, refer to NextSeq 1000/2000 Integration v2.5.0 User Interaction, Validation and Troubleshooting.
Step 1: Library Pooling and Dilution (NextSeq 1000/2000 Sequencing v2.4)
In this step, the addition of RSB dilutes pooled samples. Manually create a working pool based on the final loading concentration required.
⚠️ Create one pool per step. The Calculate Volumes automation supports one pool only.
¹ These automations are required for CLPA support only.
Master Step Fields
The following fields are defined on the Library Pooling and Dilution (NextSeq 1000/2000 Sequencing v2.4) step.
Library Pooling and Dilution (NextSeq 1000/2000 Sequencing v2.4) Master Step Field Configuration
Field Name | Field Type | Field Constraints/Options | Preset Values/Additional Options and Drop-down Items |
Final Loading Concentration (pM) | Numeric Dropdown |
| Presets
|
Final Loading Volume (ul) | Numeric |
| Default
|
Library Pool Volume (ul) | Numeric |
| Hidden |
RSB Volume for Pool (ul) | Numeric |
| Hidden |
Global Fields
The following table lists the global fields that are configured to display on the Library Pooling and Dilution (NextSeq 1000/2000 Sequencing v2.4) step.
Library Pooling and Dilution (NextSeq 1000/2000 Sequencing v2.4) Global Field Configuration
Field Name | Field Type | Field Constraints/Options | Preset Values/Additional Options and Drop-down Items |
Final Loading Concentration (pM) | Numeric Dropdown |
|
|
RSB Volume (ul) | Numeric |
|
|
Step 2: Load to Reagent Cartridge (NextSeq 1000/2000 Sequencing v2.4)
In this step, scan the reagent cartridge barcode into Clarity LIMS, then manually place the working pool into the reagent cartridge for the NextSeq 1000/2000 run. This step validates the run setup and analysis information and generates the sample sheet file and/or creates a planned run depending on the Run Mode selected.
⚠️ Use alphanumeric, dash, or underscore characters only in the submitted sample names. Any other characters can cause sample sheet validation failure in the Load to Reagent Cartridge step. The NextSeq 1000/2000 Sequencing workflow handles these characters in the Load to Reagent Cartridge step by replacing them with an underscore in the submitted sample name. The Sample Details table in the Demultiplexing step reflects the modified submitted sample name.
ℹ️ The NextSeq 1000/2000 reagent cartridges support different read cycle numbers. Make sure that the read cycle values configured for the planned run are within the maximum allowable reads for the cartridge type.
¹ These automations are required for CLPA support only.
² These automations are required for the NextSeq 1000/2000 Sequencing v2.4 workflows and contain additional logic needed for CLPA support. If you would like to remove CLPA support, contact Illumina Support.
Master Step Fields
There are 24 fields defined on the Load to Reagent Cartridge (NextSeq 1000/2000 Sequencing v2.4) step. These fields are required for sample sheet generation and planned run creation.
Load to Reagent Cartridge (NextSeq 1000/2000 Sequencing v2.4) Master Step Fields Configuration
Field Name | Field Type | Field Constraints/Options | Preset Values/Additional Options and Drop-down Items |
Run Name | Text |
| |
Instrument Type | Text Dropdown |
| Presets
|
Run Mode | Text Dropdown |
| Presets
|
Paired End | Text Dropdown |
| Presets
|
Read 1 Cycles | Numeric Dropdown |
| Presets
|
Read 2 Cycles | Numeric Dropdown |
| Presets
|
Index Reads | Text Dropdown |
| Presets
|
Index Read 1 | Numeric Dropdown |
| Presets
|
Index Read 2 | Numeric Dropdown |
| Presets
|
Analysis Workflow | Text |
| Default
|
Adapter Sequence Read 1 | Text | ||
Adapter Sequence Read 2 | Text | ||
Barcode Mismatches Index 1 | Numeric Dropdown | Presets
| |
Barcode Mismatches Index 2 | Numeric Dropdown | Presets
| |
Override Cycles | Text | ||
Cloud Run ID | Text |
| Hidden |
Use Custom Index Read 1 Primer | Toggle Switch | Default
Hidden | |
Use Custom Index Read 2 Primer | Toggle Switch | Default
Hidden | |
Use Custom Read 1 Primer | Toggle Switch | Default
Hidden | |
Use Custom Read 2 Primer | Toggle Switch | Default
Hidden Custom primer option is currently not supported. Do not enable as it will break the integration. | |
Instructions | Multiline Text |
| Default
|
Local Analysis Workflow Versions | Text Dropdown | Default
| |
Cloud Analysis Workflow Versions | Text Dropdown | Default
| |
FASTQ Compression Format | Text Dropdown |
| Presets
Default
|
Step 3: AUTOMATED - Sequencing Run (NextSeq 1000/2000 Sequencing v2.4)
This step is fully automated.
The integration starts and completes the step automatically. Data from the run is parsed back to Clarity LIMS. No user interaction is required. In this step, the pooled samples in the reagent cartridge are sequenced on the NextSeq 1000/2000 instrument.
⚠️ Do not add samples to the Ice Bucket or start or complete the step. The integration completes these actions automatically.
¹ These automations are required for CLPA support only.
Master Step Fields
There following fields are defined on the AUTOMATED - Sequencing Run (NextSeq 1000/2000 Sequencing v2.4) step. These fields are used to display the run status and sequencing run and analysis configuration parsed from the RunParameters.xml file of the sequencing run.
⚠️ Do not modify the master step field names. This action causes the integration to break.
Run Parameters and Corresponding Clarity LIMS Step Fields
The following table shows how some of the step fields map to the fields on the RunParameters.xml file, and whether the field is visible on the Record Details screen.
Master Step Field | RunParameters.xml Field | On Record Details Screen |
Current Cycle | Calculated based on CompletedCycles Field | Visible |
Current Read | Calculated based on CompletedCycles field against PlannedCycles | Visible |
Flow Cell ID | FlowCellSerialNumber | Visible |
Flow Cell Lot Number | FlowCellLotNumber | Visible |
Instrument Control Software Version | ApplicationVersion | Visible |
Instrument ID | InstrumentSerialNumber | Visible |
Output Folder | OutputFolder | Visible |
Reagent Cartridge ID | CartridgeSerialNumber | Visible |
Reagent Cartridge Lot Number | CartridgeLotNumber | Visible |
RTA Version | RtaVersion | Visible |
Run Name | ExperimentName | Visible |
Secondary Analysis Workflow | SecondaryAnalysisWorkflow | Visible |
Flow Cell Mode | FlowCellMode | Hidden |
Instrument Run ID | Derived from OutputFolder | Hidden |
Run End Time | RunEndTime | Hidden |
Run Start Time | RunStartTime | Hidden |
Secondary Analysis Mode | SecondaryAnalysisMode | Hidden |
Secondary Analysis Platform Version | SecondaryAnalysisPlatformVersion | Hidden |
SkipObdd | SkipObdd | Hidden |
Additional Master Step Fields and Values
The following table shows how the other step fields derive their values, and whether the step field is visible on the Record Details screen.
Master Step Field | Description | On Record Details Screen |
Instrument Platform |
| Visible |
Instrument Type |
| Visible |
Run Status |
| Visible |
Sequencing Log |
| Visible |
BaseSpace Run ID |
| Hidden |
¹ For information on how the integration works, refer to Run Status, Primary Metrics, and Analysis Results Parsing and Recording in How the NextSeq 1000/2000 Integration Works.
Global Fields
The following global 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 this step, the pool of samples is automatically advanced to (and queued for) the Demultiplexing (NextSeq 1000/2000 Sequencing v2.4) step.
Step 4: Demultiplexing (NextSeq 1000/2000 Sequencing v2.4)
This step is a semi-automated step.
The integration starts the step automatically and demultiplexing data from the GenerateFASTQ secondary analysis is parsed back to Clarity LIMS. The lab scientist reviews the demultiplexing result parsed into Clarity LIMS, assigns QC flags, and completes the step.
⚠️ Do not add samples to the Ice Bucket or start or complete the step. The integration completes these actions automatically.
¹ These automations are required for CLPA support only.
Master Step Fields
The following table lists the master step fields that are configured on the Demultiplexing (NextSeq 1000/2000 Sequencing v2.4) master step.
Master Step Field Configuration for Demultiplexing (NextSeq 1000/2000 Sequencing v2.4) Step
Field Name | Field Type | Field Constraints/Options | Preset Values/Additional Options and Drop-down Items |
Criteria 1 - Source Data Field | Text Dropdown | Custom Entries | Presets
|
Criteria 2 - Source Data Field | Text Dropdown | Custom Entries | Presets
|
Criteria 1 - Operator | Text Dropdown | Custom Entries | Presets
|
Criteria 2 - Operator | Text Dropdown | Custom Entries | Presets
|
Criteria 1 - Threshold Value | Numeric | Valid integer value | |
Criteria 2 - Threshold Value | Numeric | Valid integer value | |
Log | Multiline Text | Read Only | |
Analysis Completed Tim | Text | Read Only | Hidden |
Analysis Started Time | Text | Read Only | Hidden |
Analysis Status | Text | Read Only | |
BSSH Analysis ID | Text | Read Only | Hidden |
Reagent Cartridge ID | Text | Read Only | Hidden |
Global Fields
The following table lists the global fields that are configured on the Demultiplexing (NextSeq 1000/2000 Sequencing v2.4) step. These fields are used to display the demultiplexing result metrics for individual library in the sample pool.
The demultiplexing statistics are aggregated for multi-lane flow cells. For each demultiplexing field (for example, # Reads) displayed in the Sample Details table for the multi-lane flow cell (for example, P3), the displayed value is the sum of the statistics across all lanes.
Global Field Configuration for Demultiplexing (NextSeq 1000/2000 Sequencing v2.4) Step
Field Name | Field Type | Field Constraints/Options |
Index Sequence | Text | Read Only |
# One Mismatch Index Reads | Numeric | Read Only |
# Perfect Index Reads | Numeric | Read Only |
# Reads | Numeric | Read Only |
How the NextSeq 1000/2000 Integration Works
Sample Sheet Generation and Planned Run Creation
On the Load To Reagent Cartridge (NextSeq 1000/2000 Sequencing v2.4) step, when the Validate Run Setup and Create Planned Run automation is triggered, the run and analysis parameters entered in the Run Details screen are used to create a planned run. Then, the run and analysis configuration is validated. If the validation fails, an error message is sent to Clarity LIMS. If the validation passes, the sample sheet is generated (and sent back to Clarity LIMS) and/or a planned run is created depending on the Run Mode selected.
Local run mode: Only the sample sheet is generated and stored on Clarity LIMS. The sample sheet contains all the run and analysis configuration required to start the run on the instrument.
Hybrid/Cloud run mode: A planned run is created. This planned run contains all the run and analysis configuration required to start the run on the instrument. The sample sheet is also generated and stored on Clarity LIMS for reference purposes.
For details on how to start a run using different run modes, refer to Start A Sequencing Run On Instrument With Different Run Modes.
If a planned run with the same sample and project name has been created previously, the original case with the previous sample name can be reflected in the sample sheet generated from the Validate Run Setup and Create Planned Run automation. To resolve this issue, change the sample or project name in Clarity LIMS and run the automation again.
Run Status, Primary Metrics, and Analysis Results Parsing and Recording
After the sequencing run is started on the instrument, NextSeq 1000/2000 Control Software (NCS) notifies BaseSpace Sequence Hub that the sequencing run has started.
BaseSpace Sequence Hub then does the following actions:
Local run mode: Creates a run on the BaseSpace Sequence Hub database with the run configuration information received from NCS.
Hybrid/Cloud run mode: Creates a run on the BaseSpace Sequence Hub database by copying the run configuration information from the planned run using a special Cloud Run ID received from NCS.
After the run is created on BaseSpace Sequence Hub, a run update event message that carries the RunStarted equivalent message is created on BaseSpace Sequence Hub and delivered to Clarity LIMS SQS queue service. The message is captured and processed by the integration.
Based on the reagent cartridge barcode information in the event message (refer to the following example), the integration service looks in the queue of AUTOMATED - Sequencing Run (NextSeq 1000/2000 Sequencing v2.4) step for a container with the same reagent cartridge barcode. When identified, the step is started automatically and the Run Status field on Record Details screen is updated to RunStarted. The integration service then updates all the other step fields (for example, Current Read, Output Folder) by parsing the details from the RunParameters.xml uploaded to BaseSpace Sequence Hub by NCS.
How the Integration Service Handles Run Status
The NextSeq 1000/2000 Control Software (NCS) continues to notify BaseSpace Sequence Hub (BSSH) of any run status change throughout the course of the sequencing run. The run update event delivery process continues as described in the previous section.
The following table lists the run status details and how the integration service handles each status.
Run Status | Shown in Step | Details |
RunStarted | AUTOMATED - Sequencing Run (NextSeq 1000/2000 Sequencing v2.4) |
|
RunCompletedSuccessfully | AUTOMATED - Sequencing Run (NextSeq 1000/2000 Sequencing v2.4) |
|
RunErroredOut | AUTOMATED - Sequencing Run (NextSeq 1000/2000 Sequencing v2.4) |
|
RunAbortedByUser | AUTOMATED - Sequencing Run (NextSeq 1000/2000 Sequencing v2.4) |
|
AnalysisStarted | Demultiplexing (NextSeq 1000/2000 Sequencing v2.4) |
|
AnalysisCompleted | Demultiplexing (NextSeq 1000/2000 Sequencing v2.4) |
|
AnalysisFailed | Demultiplexing (NextSeq 1000/2000 Sequencing v2.4) |
|
Start A Sequencing Run On Instrument With Different Run Modes
Refer to the NextSeq 1000/2000 Product Documentation for the following information:
Configuring a run with the Proactive, Run Monitory and Storage option. Local runs are done in Local mode, and cloud or hybrid runs are done in Cloud or Hybrid mode.
Starting a local, cloud, or hybrid run.
Enabling Planned Run Generation for Samples Having Duplicate Name with Different Indexes
The library preparation workflow of the samples must be configured to ensure unique derived sample names before routing the samples through the library preparation workflow.
Re-queue Samples for Cloud Run
Clarity LIMS requires unique library names when samples are re-queued to the workflow in the NextSeq 1000/2000 integration. Assign unique names to libraries after going through library preparation.
The following steps are used to configure the library preparation workflow correctly before routing the samples for re-queuing:
From Configuration, select the Lab Work tab.
Search for the library preparation workflow used for the re-queued samples.
In the Master Step of the library preparation workflow, modify the naming convention under Step Type to generate unique library names (for example, appending LIMS ID to the default naming convention, like OutputItemLIMSID).
Select Save.
Components Installed
The following sections describe the various components that are installed by default as part of this integration. These components include the following items:
Reagent categories/label groups
Reagent kits
Control types
Containers
Information on installed workflows, protocols, steps, and automation points is provided in the Workflows, Protocols, and Steps section of NextSeq 1000/2000 Integration v2.5.0 User Interaction, Validation and Troubleshooting.
Reagent Categories/Label Groups
TruSeq HT adapters v2 (D7-D5)
Reagent Kits
Resuspension Buffer (RSB)
NextSeq 1000/2000 reagent cartridge
Container Types
Tube
96-well plate
NextSeq 1000/2000 reagent cartridge
Control Types
PhiX v3
This integration supports the NextSeq 1000/2000 reagent cartridge with barcode provided in the format [A-Z]{2}[0-9]{7}-[A-Z0-9]{4} (for example, EC1234567-EC03).
Rules and Constraints
⚠️ The NextSeq 1000/2000 Reagent Cartridge barcode should not be modified after a successful validation. Modifications can cause issues when Clarity LIMS tries to update the status and sample details of subsequent steps.
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:
Which samples, and how many, can enter each step together.
Which samples, and how many, can be pooled together.
The NextSeq 1000/2000 reagent cartridge barcode must be unique. There should not be multiple NextSeq 1000/2000 reagent cartridge containers in the system with the same name.
Reagent labels (indexes) must be unique.
One library pool can only contain one library or control with no label (index).
Do not manually start or complete the AUTOMATED - Sequencing Run (NextSeq 1000/2000 Sequencing v2.4) step. This step is a fully automated step, and the integration service does not update samples correctly if they have been manually started.
Do not manually start the Demultiplexing (NextSeq 1000/2000 Sequencing v2.4) step. This step is semi-automated, and the integration service does not update the demultiplexing result correctly if they have been manually started.
For the automated run to start successfully, select Validate Run Setup and Create Planned Run in the Load to Reagent Cartridge step.
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