Configuration
Last updated
Last updated
The Illumina NovaSeq 6000 Integration Package v2.6 supports the integration of Clarity LIMS to NovaSeq 6000 instruments.
This document describes the integration and includes information about the preconfigured protocols, steps, automations, installed components, configuration requirements, rules, and constraints.
For instructions on user interaction for each step, validating and troubleshooting the Illumina NovaSeq 6000 Integration, refer to NovaSeq 6000 Integration v2.6.0 User Interaction, Validation and Troubleshooting.
The configuration provided in this integration has been established to support NovaSeq 6000 lab processes. Any configuration changes to protocols or workflows—including renaming protocols, steps, and fields—could break the process.
It is assumed that samples enter the NovaSeq 6000 v2.3 workflow as normalized libraries. That is, before they are assigned to the workflow the following actions occur:
Samples have been accessioned into Clarity LIMS.
Samples have been run through QC and library prep.
Samples have been normalized, and the value is captured in a field called Normalized Molarity (nM).
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.
The Illumina NovaSeq 6000 Integration Package v2.6.0 includes two workflows:
NovaSeq Validation Library Prep (NovaSeq 6000 v2.3)
NovaSeq 6000 v2.3
The NovaSeq Validation Library Prep (NovaSeq 6000 v2.3) workflow allows for validation of the system after installation is complete. For details, refer to NovaSeq 6000 Integration v2.6.0 User Interaction, Validation and Troubleshooting.
This protocol sets the Loading Workflow Type and allows you to choose the appropriate Flowcell Type and Final Loading Concentration(pM). At the end of the protocol, a routing script sends the normalized libraries to either the NovaSeq Standard (NovaSeq 6000 v2.3) or the NovaSeq Xp (NovaSeq 6000 v2.3) protocol.
This protocol contains one step: Define Run Format (NovaSeq 6000 v2.3).
Step input: NTP (normalized libraries)
Step output: None
The following table provides field configuration details for the fields defined on the Define Run Format (NovaSeq 6000 v2.3) step.
Define Run Format (NovaSeq 6000 v2.3) Master Step Field Configuration
The following table lists the global fields that are configured to display on the Define Run Format (NovaSeq 6000 v2.3) step.
Global Field Configuration (Derived Sample)
Samples are routed to this protocol if the Loading Workflow Type value is set to NovaSeq Standard. Samples are pooled and added to a library tube in preparation for the NovaSeq run.
At the end of this protocol, a routing script sends the library tube to the AUTOMATED - NovaSeq Run (NovaSeq 6000 v2.3) protocol.
This protocol contains two steps:
Make Bulk Pool for NovaSeq Standard (NovaSeq 6000 v2.3)
Dilute and Denature (NovaSeq 6000 v2.3)
In this step, manually place libraries into a single pool. Resuspension buffer and reagents are added.
Step input: NTP (normalized libraries)
Step output: Bulk pool
The following automations are configured on the step (in the order they are triggered at run time).
The following table provides field configuration details for the fields defined on the Make Bulk Pool for NovaSeq Standard (NovaSeq 6000 v2.3) step.
Make Bulk Pool for NovaSeq Standard (NovaSeq 6000 v2.3) Master Step Field Configuration
The following table lists the global fields that are configured to display on the Make Bulk Pool for NovaSeq Standard (NovaSeq 6000 v2.3) step.
Global Field Configuration (Derived Sample)
In this step, pooled samples are denatured and diluted by the addition of NaOH, Tris-HCl, and Resuspension Buffer (RSB). Samples are manually placed into the library tube that is used in the NovaSeq run. In addition, this step generates the sample sheet file and the run recipe (*json file) needed to start the NovaSeq run. The step input is Bulk pool, and the step output is Library tube.
The following table provides field configuration details fields defined on the Dilute and Denature (NovaSeq 6000 v2.3) step. These fields are required for sample sheet and JSON file generation.
Dilute and Denature (NovaSeq 6000 v2.3) Master Step Field Configuration
The following table lists the global step fields that are configured to display on the Dilute and Denature (NovaSeq 6000 v2.3) step.
Global Field Configuration (Derived Sample)
Samples are routed to this protocol if the Loading Workflow Type value is set to NovaSeq Xp.
Samples are pooled and added to lanes on the NovaSeq flow cell type selected in the Define Run Format (NovaSeq 6000 v2.3) step.
At the end of the protocol, a routing script sends the flow cell to the AUTOMATED - NovaSeq Run (NovaSeq 6000 v2.3) protocol.
This protocol contains three steps:
Step 1: Make Bulk Pool for NovaSeq Xp (NovaSeq 6000 v2.3)
Step 2: Dilute, Denature & ExAmp (NovaSeq 6000 v2.3)
Step 3: Load to Flowcell (NovaSeq 6000 v2.3)
In this step, the libraries are manually placed into a pool. The step input is NTP (normalized libraries) and the step output is Bulk pool.
These automations are described in the order in which they are triggered at run time.
Calculates the Per Sample Volume (ul) to be added to the pool:
If the smallest Per Sample Volume (ul) value is less than 5, Clarity LIMS automatically assigns a value of 5 to the sample's Adjusted Per Sample Volume (ul) field.
Clarity LIMS then adjusts the Adjusted Per Sample Volume (ul) field value for all other samples in the batch, based on the ratio used to increase the lowest value to 5.
Calculates the Total Sample Volume (ul) field value:
If the Total Sample Volume is less than the Bulk Pool Volume, calculates the RSB Volume (ul) field value:
Copies the Flowcell Type and Loading Workflow Type values from the step inputs to the step outputs:
Uses the NovaSeq_Xp_Bulk_Pool.csv and NovaSeq_Xp_Bulk_Pool2.csv template files to generate a single CSV file containing information about the bulk pool and the samples it contains. The generated file is available for download on the Step Setup screen of the following step—Dilute, Denature & ExAmp (NovaSeq 6000 v2.3).
Resets the Total Sample Volume (ul) and Number of Samples in Pool field values so that the automation is idempotent:
The following table provides field configuration details for the fields defined on the Make Bulk Pool for NovaSeq Xp (NovaSeq 6000 v2.3) step.
Make Bulk Pool for NovaSeq Xp (NovaSeq 6000 v2.3) Master Step Field Configuration
The following table lists the global fields that are configured to display on the Make Bulk Pool for NovaSeq Xp (NovaSeq 6000 v2.3) step.
Global Field Configuration (Derived Sample)
In this step, pooled samples are denatured and diluted by the addition of DPX, NaOH, Tris-HCl, and RSB. Manually create working pools based on the number of lanes you want to sequence. The step input is Bulk pool and the step output is Working pool. Working pool is a variable number for how many working pools need to be created per bulk pool.
These automations are described in the order in which they are triggered at run time.
The following table provides field configuration details for the fields defined on Dilute, Denature & ExAmp (NovaSeq 6000 v2.3) step. These field values are set by a script and are not editable while running the step.
Dilute, Denature & ExAmp (NovaSeq 6000 v2.3) Master Step Field Configuration
The following table lists the global fields that are configured to display on the Dilute, Denature & ExAmp (NovaSeq 6000 v2.3) step.
Global Field Configuration (Derived Sample)
In this step, scan the flow cell barcode into Clarity LIMS, then manually place the working pools into the lanes of the flow cell that is used in the NovaSeq run. The step input is Working pool and the step output is Flow cell (output containers: S1 and S2 with 2 lanes, and S4 with 4 lanes).
These automations are described in the order in which they are triggered at run time.
The following table provides field configuration details for the fields defined on the Load to Flowcell (NovaSeq 6000 v2.3) step.
Load to Flowcell (NovaSeq 6000 v2.3) Master Step Field Configuration
The following table lists the global fields (derived samples) that are configured to display on the Load to Flowcell (NovaSeq 6000 v2.3) step.
This final protocol contains one fully automated step, AUTOMATED - NovaSeq Run (NovaSeq 6000 v2.3).
Step input: Library tube from the NovaSeq Standard protocol or flow cell from the NovaSeq Xp protocol.
Step output: Result file and measurement.
In this step, pooled samples are sequenced on the NovaSeq instrument. The run data network folder is monitored by the sequencing service and automation worker to determine when the sequencing run begins and ends.
When a run is initiated on the NovaSeq instrument, the NovaSeq Control Software (NVCS) looks for the sample sheet and run recipe (*.json file) on the shared network drive.
The NVCS copies the sample sheet to the run directory.
The NVCS uses the run recipe to start the sequencing run.
When the run starts:
The instrument software creates a new run folder (named <libraryID>) on the shared network drive and copies the following files into that folder:
RunParameters.xml
RunInfo.xml
LIMS/<libraryID>.json file (run recipe)
The Real-Time Analysis v3 (RTA3) software creates the InterOp folder.
The sequencing service detects the presence of the RunParameters, RunInfo, and JSON files and starts the AUTOMATED- NovaSeq Run (NovaSeq 6000 v2.3) step in Clarity LIMS.
As the run progresses, the InterOp data files are filled in.
At the end of the run, the NovaSeq:
Copies the run data files to the InterOp folder.
Creates the CopyComplete.txt file in the run folder. This step indicates to the sequencing service that the run has completed and the data files are ready.
The sequencing service triggers the Read InterOp Metrics automation. This automation reads the files, records the parsed metrics into Clarity LIMS, and finally completes the step in Clarity LIMS.
The fields defined on the AUTOMATED - NovaSeq Run (NovaSeq 6000 v2.3) step are listed in the Clarity LIMS Configuration area (Custom Fields > Master Step Fields tab).
The following table shows how the parsed RunParameters.xml fields map to step fields configured on the AUTOMATED - NovaSeq Run (NovaSeq 6000 v2.3) step in Clarity LIMS.
Fields Parsed by parse_novaseq_run_parameters script
The global fields that are configured to support the parsing of key metrics back into Clarity LIMS are as follows.
Yield PF (Gb) R1
Yield PF (Gb) R2
Reads PF (M) R1
Reads PF (M) R2
Cluster Density (K/mm^2) R1
Cluster Density (K/mm^2) R2
%PF R1
%PF R2
% Bases >=Q30 R1
% Bases >=Q30 R2
Intensity Cycle 1 R1
Intensity Cycle 1 R2
% Phasing R1
% Phasing R2
% Prephasing R1
% Prephasing R2
% Aligned R1
% Aligned R
% Error Rate R1
% Error Rate R2
The following sections describe the various components that are installed by default as part of this integration. These components include files, properties, reagent categories/label groups, reagent kits, and containers. Information on installed workflows, protocols, steps, and automation points is provided in the previous Workflows, Protocols, and Steps section.
The Illumina NovaSeq 6000 Integration v2.6.0 Package is distributed as two RPM packages:
BaseSpaceLIMS-novaseq-extensions
BaseSpaceLIMS-novaseq-sequencing-service
The RPM packages install the components listed in the following table.
The NovaSeq 6000 Integration requires installation of NGS Extensions Package v5.25.0 or later.
If the NGS Extensions Package is not already installed, or if a version earlier than v5.25.0 is installed, the latest version is installed by default with the NovaSeq integration. For details, refer to NovaSeq 6000 Integration v2.6.0 Release Notes.
If NGS Extensions Package v5.25.0 is already installed, upgrade is not forced or required.
Secret Util Package is required for the NGS Extensions Package v5.25.0.
If the Secret Util Package is not already installed, then Secret Util package is installed along with the installation of NGS Extension Package v5.25.0.
If the Secret Util Package is already installed, upgrade is not forced or required.
Illumina NovaSeq 6000 Integration v2.6.0 RPM Components
Refer to Integration Properties Details for the properties installed with the integration package.
The NovaSeq 6000 Integration v2.6.0 Package installs the following label groups, reagent kits, and container types.
TruSeq HT Adapters v2 (D7-D5)
DPX1
DPX2
DPX3
Resuspension Buffer (RSB)
NaOH
Tris-HCl
Library Tube
S1
S2
S4
SP
The following are instructions for configuring the NovaSeq instrument for the Clarity LIMS integration:
Launch NovaSeq Control Software.
On the home screen, select the menu (top left) and select Settings.
Select File-Based and enter the network folder location that NovaSeq Control Software retrieves the JSON recipe from.
Enter the network output folder location.
Select Save.
For more information, refer to the NovaSeq 6000 Sequencing System Guide at support.illumina.com.
The requirements for the routing script functionality are as follows.
On the steps that use the routing script — Define Run Format (NovaSeq 6000 v2.3) and Dilute and Denature (NovaSeq 6000 v2.3) — the Next Step for all samples must be set to Remove from workflow. This value is set by a script. Do not change this value in the Assign Next Steps screen.
In the protocol configuration screen, the following setting is required and must not be changed.
In the Next Steps section for the last step in the protocol, the method of assigning the next step must be set to Automatic.
Sample sheet and run recipe file generation occurs on the step before the run—Dilute and Denature (NovaSeq 6000 v2.3) in the NovaSeq Standard protocol or Load to Flowcell (NovaSeq 6000 v2.3) in the NovaSeq Xp protocol. This step is where samples are placed on the library tube or flow cell that is loaded in the NovaSeq instrument.
In the default configuration, the Generate Sample Sheet & Run Recipe automation generates the following:
One CSV format sample sheet file for use bcl2fastq v2.20 downstream analysis
One JSON format run recipe file
The Prepare Files for NovaSeq automation places the generated files on the NAS where the instrument uses them to start the run.
The integration supports the following container types:
Library tube with barcode provided in the following format:
[A-Z]{2}[0-9]{7}-[A-Z]{3}
Example — NV1234567-LIB
Flow cell with barcode provided in one of the following formats:
For SP and S1 — [A-Z0-9]{5}DR[A-Z0-9]{2}
For S2 — [A-Z0-9]{5}DM[A-Z0-9]{2}
For S4 — [A-Z0-9]{5}DS[A-Z0-9]{2}
Example S2 flow cell barcode — H1234DMXX
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 the following information:
Which samples, and how many, can enter each step together.
Which samples, and how many, can be pooled together.
Reagent labels (indexes) must be unique.
The library tube ID must be unique. There should not be multiple library tube containers in the system with the same name.
Only controls are permitted as unindexed samples. All other unindexed samples and pools are not permitted.
Refer to the Bcl2fastq2 Sample Sheet Generation section of the Illumina Instrument Sample Sheets (NGS v5.17 & later) document for detailed information on the following:
Sample sheet generation script parameters and usage
Sample sheet data and configuration options
Enabling unique FASTQ file names per sequencing run
Do not manually start the AUTOMATED - NovaSeq Run (NovaSeq 6000 v2.3) step. This step is fully automated. If the samples have been manually started, the sequencing service may not update them correctly.
The output folder must be readable by the Clarity LIMS glsjboss account on the server.
Do not add samples to the Ice Bucket or start the step. The integration does this action automatically.
Only create one pool per step.
To ensure accurate pipetting of each sample in a pool for sequencing, the Per Sample Volume (ul) value must be equal to or higher than the Minimum Per Sample Volume (ul). The default value is set at 5, which can be edited. Assuming the default Minimum Per Sample Volume (ul) value of 5, for a given batch:
Not used. This functionality is handled by the Clarity LIMS configuration for pooling
Only create one pool per step.
To ensure accurate pipetting of each sample in a pool for sequencing, the Per Sample Volume (ul) value must be equal to or higher than the Minimum Per Sample Volume (ul). The default value set at 5 and can be edited. Assuming the default Minimum Per Sample Volume (ul) value of 5, for a given batch:
Not used. This functionality is handled by the Clarity LIMS configuration for pooling.
Do not add samples to the Ice Bucket or start the step manually. This is a fully automated step. The sequencing service may not update samples correctly if they have been manually started.
Do not disable Update Lane Number automation as it causes run metric parsing to work improperly.
Field Name
Field Type
Options
Additional Options and Dropdown Items
Adjusted Per Sample Volume (ul)
Numeric
Read Only
Decimal places displayed = 2
Final Loading Concentration (pM)
Numeric Dropdown
Required Field
Custom Entries
Presets
225
400
Decimal places displayed = 0
Flowcell Type
Text Dropdown
Required Field
Presets
S1
S2
S4
SP
Loading Workflow Type
Text Dropdown
Required Field
Presets
NovaSeq Standard
NovaSeq Xp
[Remove from workflow]
Minimum Molarity (nM)
Numeric
Decimal places displayed = 2
Normalized Molarity (nM)
Numeric
Decimal places displayed = 2
Per Sample Volume (ul)
Numeric
Read Only
Decimal places displayed = 2
Warning
Text Dropdown
Read Only
Custom Entries
Presets
The Normalized Molarity (nM) is too low.
n/a
Field Name
Field Type
Options
Additional Options and Drop-Down Items
Flowcell Type
Text Dropdown
Required Field
Presets
S1
S2
S4
SP
Loading Workflow Type
Text Dropdown
Required Field
Presets
NovaSeq Standard
NovaSeq Xp
[Remove from workflow]
Field Name
Field Type
Field Constraints/Options
Preset Values/Additional Options and Drop-Down Items
RSB Volume (ul)
Numeric
Read Only
Decimal places displayed = 2
Flowcell Type
Text Dropdown
Required Field
Presets
S1
S2
S4
SP
Loading Workflow Type
Text Dropdown
Required Field
Presets
NovaSeq Standard
NovaSeq Xp
[Remove from workflow]
Field Name
Field Type
Options
Additional Options and Drop-Down Items
DPX1 Volume (ul)
Numeric
Read Only
Decimal places displayed = 0
DPX2 Volume (ul)
Numeric
Read Only
Decimal places displayed = 0
DPX3 Volume (ul)
Numeric
Read Only
Decimal places displayed = 0
Field Name
Field Type
Field Constraints/Options
Preset Values/Additional Options and Drop-Down Items
BP Aliquot Volume (ul)
Numeric
Read Only
Decimal places displayed = 0
Flowcell Type
Text Dropdown
Required Field
Presets
SP
S1
S2
S4
Loading Workflow Type
Text Dropdown
Required Field
Presets
NovaSeq Standard
NovaSeq Xp
[Remove from workflow]
Mastermix per Lane (ul)
Numeric
Read Only
Decimal places displayed = 0
NaOH Volume (ul)
Numeric
Read Only
Decimal places displayed = 2
Tris-HCl Volume (ul)
Numeric
Read Only
Decimal places displayed = 2
Field Name
Field Type
Options
Additional Options and Drop-Down Items
Flowcell Type
Text Dropdown
Required Field
Presets
S1
S2
S4
SP
RunParameters.xml Field
Field Name
FlowCellSerialBarcode
Flow Cell ID
FlowCellPartNumber
Flow Cell Part Number
FlowCellLotNumber
Flow Cell Lot Number
FlowCellExpirationdate
Flow Cell Expiration Date
FlowCellMode
Flow Cell Mode
RunId
Run ID
ClusterSerialBarcode
PE Serial Barcode
ClusterPartNumber
PE Part Number
ClusterLotNumber
PE Lot Number
ClusterExpirationdate
PE Expiration Date
ClusterCycleKit
PE Cycle Kit
SbsSerialBarcode
SBS Serial Barcode
SbsPartNumber
SBS Part Number
SbsLotNumber
SBS Lot Number
SbsExpirationdate
SBS Expiration Date
SbsCycleKit
SBS Cycle Kit
BufferSerialBarcode
Buffer Serial Barcode
BufferPartNumber
Buffer Part Number
BufferLotNumber
Buffer Lot Number
BufferExpirationdate
Buffer Expiration
OutputRunFolder
Output Folder
WorkflowType
Loading Workflow Type
Files Installed
Location
Description
configure_extensions_novaseq.sh
/opt/gls/clarity/config/
Script that imports Clarity LIMS configuration into the application database and updates property values.
novaseq-extensions.jar
/opt/gls/clarity/extensions/novaseq
Jar file containing API-based Clarity LIMS extensions used throughout the protocols.
novaseq-sequencing.jar
/opt/gls/clarity/extensions/novaseq/SequencingService
Sequencing service jar file that captures the run results.
novaseq-remote-extensions.jar
/opt/gls/clarity/extensions/novaseq
Jar file containing scripts that require access to the run folders on the NAS.
InterOp libraries
/opt/gls/clarity/extensions/novaseq/lib
Illumina shared library for parsing InterOp data files.
NovaSeq_Standard_Bulk_Pool1.csv NovaSeq_Standard_Bulk_Pool2.csv NovaSeq_Standard_Bulk_Pool3.csv NovaSeq_Xp_Bulk_Pool.csv NovaSeq_Xp_Bulk_Pool2.csv NovaSeq_Xp_Working_Pool.csv NovaSeq_Xp_Working_Pool2.csv
/opt/gls/clarity/extensions/novaseq/Templates
Template files used for file generation throughout the protocols.
Field Name
Field Type
Field Constraints/Options
Preset Values/Additional Options and Drop-Down Items
Comment
Multiline Text
None
Instruction
Text
Read Only
Default
Add Flowcell Type and Loading Workflow Type below
Flowcell Type
Text Dropdown
Required Field
Custom Entries
Presets
S1
S2
S3
S4
Loading Workflow Type
Text Dropdown
Required Field
Presets
NovaSeq Standard
NovaSeq Xp
Field Name
Field Type
Options
Additional Options and Drop-Down Items
% PhiX (2.5nM) Spike-In
Numeric
Range = 1–100
Decimal places displayed = 0
Bulk Pool Volume (ul)
Numeric
Decimal places displayed = 2
Minimum Per Sample Volume (uL)
Numeric
Required Field
Default
5
Decimal places displayed = 2
Number of Flowcells to Sequence
Numeric
Required Field
Range = 1–10
Decimal places displayed = 0
Number of Samples in Pool
Numeric
Default
0
Decimal places displayed = 0
PhiX Volume (ul)
Numeric
Decimal places displayed = 2
Total Sample Volume (ul)
Numeric
Default
0
Decimal places displayed = 2
Calculate Volumes Script
Text
Required Field
Read Only
Default value provided in the drop-down section following the table.
Field Name
Field Type
Options
Additional Options and Drop-Down Items
Flowcell Type
Text Dropdown
Required Field
Presets
S1
S2
S4
SP
Loading Workflow Type
Text Dropdown
Required Field
Presets
NovaSeq Standard
NovaSeq Xp
[Remove from workflow]
NaOH Volume (ul)
Numeric
Read Only
Decimal places displayed = 2
RSB Volume (ul)
Numeric
Read Only
Decimal places displayed = 2
Tris-HCl Volume (ul)
Numeric
Read Only
Decimal places displayed = 2
Volume of Pool to Denature (ul)
Numeric
Read Only
Decimal places displayed = 0
Field Name
Field Type
Options
Additional Options and Drop-Down Items
BaseSpace Sequence Hub Configuration
Text Dropdown
Required Field
Presets
Not Used
Run Monitoring Only
Run Monitoring and Storage
Experiment Name
Text
Required Field
Index Read 1
Numeric Dropdown
Required Field
Custom Entries
Range = 0–20
Decimal places displayed = 0
Presets
0
6
8
Index Read 2
Numeric Dropdown
Required Field
Custom Entries
Range = 0–20
Decimal places displayed = 0
Presets
0
6
8
Paired End
Text Dropdown
Required Field
Presets
True
False
Read 1 Cycles
Numeric Dropdown
Required Field
Custom Entries
Range = 1–251
Decimal places displayed = 0
Presets
251
151
101
51
Read 2 Cycles
Numeric Dropdown
Required Field
Custom Entries
Range = 0–251
Decimal places displayed = 0
Presets
251
151
101
51
Reverse Complement Workflow
Toggle Switch
Required Field
Default
Yes
Run Mode
Text Dropdown
Read Only
Presets
SP
S1
S2
S4
Sample Sheet Path
Text
Read Only
UMI - Read 1 Length
Numeric
Range = 1
Decimal places displayed = 0
UMI - Read 1 Start From Cycle
Numeric
Range = 1
Decimal places displayed = 0
UMI - Read 2 Length
Numeric
Range = 1
Decimal places displayed = 0
UMI - Read 2 Start From Cycle
Numeric
Range = 1
Decimal places displayed = 0
Use Custom Index Read 1 Primer
Toggle Switch
Default
No
Use Custom Read 1 Primer
Toggle Switch
Default
No
Use Custom Read 2 Primer
Toggle Switch
Default
No
Workflow
Text
Read Only
Default
GenerateFASTQ
Workflow Type
Text Dropdown
Required Field
Presets
No Index
Single Index
Dual Index
Field Name
Field Type
Options
Additional Options and Drop-Down Items
% PhiX (0.25nM) Spike-In
Numeric
Range = 0–100
Decimal places displayed = 0
Bulk Pool Volume (ul)
Numeric
Decimal places displayed = 2
Minimum Per Sample Volume (ul)
Numeric
Required Field
Default
5
Decimal places displayed = 2
Number of Lanes to Sequence
Numeric
Required Field
Decimal places displayed = 0
Number of Sample in Pool
Numeric
Default
0
Decimal places displayed = 0
PhiX Volume (ul)
Numeric
Decimal places displayed = 2
Total Sample Volume (ul)
Numeric
Default
0
Decimal places displayed = 0
Field Name
Field Type
Options
Additional Options and Drop-Down Items
BaseSpace Sequence Hub Configuration
Text Dropdown
Required Field
Presets
Not Used
Run Monitoring Only
Run Monitoring and Storage
Experiment Name
Text
Required Field
Index Read 1
Numeric Dropdown
Required Field
Custom Entries
Range = 0–20
Decimal places displayed = 0
Presets
0
6
8
Index Read 2
Numeric Dropdown
Required Field
Custom Entries
Range = 0–20
Decimal places displayed = 0
Presets
0
6
8
Library Tube Barcode
Text
Required Field
Paired End
Text Dropdown
Required Field
Presets
True
False
Read 1 Cycles
Numeric Dropdown
Required Field
Custom Entries
Range = 1–251
Decimal places displayed = 0
Presets
251
151
101
51
Read 2 Cycles
Numeric Dropdown
Required Field
Custom Entries
Range = 0–251
Decimal places displayed = 0
Presets
251
151
101
51
Reverse Complement Workflow
Toggle Switch
Required Field
Default
Yes
Run Mode
Text Dropdown
Read Only
Presets
SP
S1
S2
S4
Sample Sheet Path
Text
Read Only
UMI - Read 1 Length
Numeric
Range = 1
Decimal places displayed = 0
UMI - Read 1 Start From Cycle
Numeric
Range = 1
Decimal places displayed = 0
UMI - Read 2 Length
Numeric
Range = 1
Decimal places displayed = 0
UMI - Read 2 Start From Cycle
Numeric
Range = 1
Decimal places displayed = 0
Use Custom Index Read 1 Primer
Toggle Switch
Default
No
Use Custom Read 1 Primer
Toggle Switch
Default
No
Use Custom Read 2 Primer
Toggle Switch
Default
No
Workflow
Text
Read Only
Default
GenerateFASTQ
Workflow Type
Text Dropdown
Required Field
Presets
No Index
Single Index
Dual Index
(does not show on Record Details screen)
Hidden (does not show on Record Details screen)
For calculation purposes, not displayed
For calculation purposes, not displayed
For calculation purposes, not displayed
For calculation purposes, not displayed
Do not remove this field. It is used by the Calculate Volumes automation script.
Used in Make Bulk Pool for NovaSeq Standard (NovaSeq 6000 v2.3) step only. Displays on Record Details screen and in the generated CSV file.
The value of 251 is only supported for SP flow cell type. For all other flow cell types, the maximum value is 151.
The value of 251 is only supported for SP flow cell type. For all other flow cell types, the maximum value is 151.
Not displayed in user interface
For calculation purposes, not displayed
For calculation purposes, not displayed
For calculation purposes, not displayed
For calculation purposes, not displayed
The value of 251 is only supported for SP flow cell type. For all other flow cell types, the maximum value is 151.
The value of 251 is only supported for SP flow cell type. For all other flow cell types, the maximum value is 151.
Not displayed in user interface