For the complete documentation index, see llms.txt. This page is also available as Markdown.

NovaSeq X Series Sequencing v2.0

Protocol 1: NovaSeq X Series Sequencing v2.0

Protocol Type = Sequencing

Next Steps Configuration

  • Step(s):

    • 1: Assign Analysis Configuration Template (NovaSeq X Series Sequencing v2.0)

      • Start Next Step = Manual

      • Assign Next Step = Automatic

    • 2: Make Bulk Pool (NovaSeq X Series Sequencing v2.0)

      • Start Next Step = Manual

      • Assign Next Step = Automatic

    • 3: Dilute and Denature (NovaSeq X Series Sequencing v2.0)

      • Start Next Step = Manual

      • Assign Next Step = Automatic

    • 4: Load to Library Tube Strip (NovaSeq X Series Sequencing v2.0)

      • Start Next Step = Manual

      • Assign Next Step = Automatic

    • 5: AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v2.0)

      • Start Next Step = Manual

      • Assign Next Step = Automatic

    • 6: AUTOMATED - Analysis Run (NovaSeq X Series Sequencing v2.0)

      • Assign Next Step = Manual

Step

To Step 1

To Step 2

To Step 3

To Step 4

To Step 5

To Step 6

1

2

3

4

5

6

Step 1: Assign Analysis Configuration Template (NovaSeq X Series Sequencing v2.0)

  • Master Step Name = Assign Analysis Configuration Template (NovaSeq X Series Sequencing v2.0)

  • Step Type = No Outputs

  • Instrument Types

    • NovaSeq X Series

      • Vendor = Illumina

The version of Assign Analysis Configuration Template (NovaSeq X Series Sequencing) master step name may be different depending on the version of IPP installed.

Automations

Validate Sample Names and Register Step Started
  • Trigger Location = Step

  • Trigger Style = Automatic upon entry

1. Retrieve ACT List
  • Trigger Location = Record Details

  • Trigger Style = Manual button

2. Retrieve ACT Information
  • Trigger Location = Record Details

  • Trigger Style = Manual button

Apply Selected ACT to Samples and Set Next Step
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

ℹ The actual version of workflow(s) and/or step(s) used in the automation script may be different depending on the version of IPP installed.

Register Step Completed
  • Trigger Location = Step

  • Trigger Style = Automatic upon exit

Queue

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Analysis Configuration Template

    Text

    Default = No Analysis

    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

    Skip Pooling

    Toggle Switch

    Required Field

    Default = False

  • Sample Table

    • Sample Display Default = Collapse

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      ACT Name

      Text

      Read Only

      Derived Sample

      Molarity (nM)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Sample Name

      Built-in

Step 2: Make Bulk Pool (NovaSeq X Series Sequencing v2.0)

  • Master Step Name = Make Bulk Pool (NovaSeq X Series Sequencing v2.0)

  • Step Type = Pooling

  • Aliquot Generation = Fixed, 1

  • Naming Convention = {PoolName}

  • Reagent Kits

    • Resuspension Buffer (RSB)

The version of Make Bulk Pool (NovaSeq X Series Sequencing) master step name may be different depending on the version of IPP installed.

Automations

Register Step Started
  • Trigger Location = Step

  • Trigger Style = Automatic upon entry

Validate Analysis Configurations
  • Trigger Location = Pooling

  • Trigger Style = Automatic upon exit

Calculate Volumes
  • Trigger Location = Record Details

  • Trigger Style = Manual button

Set Next Step
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

Register Pools and Register Step Completed
  • Trigger Location = Step

  • Trigger Style = Automatic upon exit

Queue

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Pooling

  • Label Uniqueness = On

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Final Loading Concentration (pM)

    Numeric

    Required Field

    • Presets

      • 90

      • 140

      • 150

      • 160

      • 180

    • Decimal Places Displayed = 0

    Flowcell Type

    Text Dropdown

    Required Field

    Presets

    • 1.5B

    • 5B

    • 10B

    • 25B

    Minimum Per Sample Volume (ul)

    Numeric

    Required Field

    • Default = 2

    • Decimal Places Displayed = 2

    Number of Lanes to Sequence

    Numeric

    Required Field

    Decimal Places Displayed = 0

  • Sample Table

    • Sample Display Default = Collapse

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Derived Sample

      Final Loading Concentration (pM)

      Numeric

      Required Field

      • Presets

        • 225

        • 400

      • Decimal Places Displayed = 0

      Derived Sample

      NovaSeq X Flowcell Type

      Text Dropdown

      Required Field

      Presets

      • 1.5B

      • 5B

      • 10B

      • 25B

      Derived Sample

      RSB Volume (ul)

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 3: Dilute and Denature (NovaSeq X Series Sequencing v2.0)

  • Master Step Name = Dilute and Denature (NovaSeq X Series Sequencing v2.0)

  • Step Type = Standard

  • Derived Sample Generation = Variable, 2

  • Naming Convention = {InputItemName}_WP{OutputItemNumber}

  • Reagent Kits

    • NaOH

    • Resuspension Buffer (RSB)

    • TT2

The version of Dilute and Denature (NovaSeq X Series Sequencing) master step name may be different depending on the version of IPP installed.

Automations

Copy Custom Fields and Register Step Started
  • Trigger Location = Step

  • Trigger Style = Automatic upon entry

Calculate Volumes
  • Trigger Location = Record Details

  • Trigger Style = Manual button

Set Next Step
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

Register Step Completed
  • Trigger Location = Step

  • Trigger Style = Automatic upon exit

Queue

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    1-2% PhiX Spike-In

    Toggle Switch

    Required Field

    Default = False

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Derived Sample

      BP Aliquot Volume (ul)

      Numeric

      Read Only

      Decimal Places Displayed = 1

      Derived Sample

      Final Loading Concentration (pM)

      Numeric

      Required Field

      • Presets

        • 225

        • 400

      • Decimal Places Displayed = 0

      Derived Sample

      NaOH Volume (ul)

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Derived Sample

      NovaSeq X Flowcell Type

      Text Dropdown

      Required Field

      Presets

      • 1.5B

      • 5B

      • 10B

      • 25B

      Derived Sample

      RSB Volume (ul)

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      TT2 Volume (ul)

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Project

      Project Name

      Built-in

Step 4: Load to Library Tube Strip (NovaSeq X Series Sequencing v2.0)

  • Master Step Name = Load to Library Tube Strip (NovaSeq X Series Sequencing v2.0)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

The version of Load to Library Tube Strip (NovaSeq X Series Sequencing) master step name may be different depending on the version of IPP installed.

Automations

Validate Flowcell Inputs, Analysis Configurations and Register Step Started
  • Trigger Location = Step

  • Trigger Style = Automatic upon entry

Validate Library Tube Strip Barcode
  • Trigger Location = Placement

  • Trigger Style = Automatic upon exit

Validate Run Setup and Create Sample Sheet
  • Trigger Location = Record Details

  • Trigger Style = Manual button

Set Next Step
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

Register Step Completed
  • Trigger Location = Step

  • Trigger Style = Automatic upon exit

Queue

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Instrument ID

    ℹ Only applicable for on-premise integration

    Text

    Read Only

    Derived Sample

    NovaSeq X Flowcell Type

    Text Dropdown

    Required Field

    Presets

    • 1.5B

    • 5B

    • 10B

    • 25B

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    NovaSeq X Flowcell Type

    Text Dropdown

    Required Field

    Presets

    • 1.5B

    • 5B

    • 10B

    • 25B

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Placement = Enabled

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

    • Placement Pattern = Row

  • Destination Containers

    • Library 2-tube Strip

      • Rows

        • Number: 1

        • Naming: Numeric

        • Start at: 1

      • Columns

        • Number: 1

        • Naming: Numeric

        • Start at: 1

    • Library 8-tube Strip

      • Rows

        • Number: 1

        • Naming: Numeric

        • Start at: 1

      • Columns

        • Number: 1

        • Naming: Numeric

        • Start at: 1

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    BCL Convert Version

    Text

    Create Planned Run

    Toggle Switch

    Required Field

    Default = True

    Index 1 Cycles

    Numeric

    Required Field

    Presets

    • 0

    • 6

    • 8

    Index 2 Cycles

    Numeric

    Required Field

    Presets

    • 0

    • 6

    • 8

    Instrument

    ℹ Only applicable for on-premise integration.

    Text

    Read Only

    Read 1 Cycles

    Numeric

    Required Field

    Presets

    • 51

    • 101

    • 151

    • 301

    Read 2 Cycles

    Numeric

    Required Field

    Presets

    • 51

    • 101

    • 151

    • 301

    Run Name

    Text

    Required Field

  • Sample Table

    • Sample Display Default = Collapse

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 5: AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v2.0)

  • Master Step Name = AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v2.0)

  • Step Type = Analysis

  • Measurement Generation = Fixed, 1

  • Naming Convention = Lane {InputWellLocation:0,1}

  • Reagent Kits

    • Buffer Cartridge

      • Supplier = Illumina

    • Lyophilization Cartridge

      • Supplier = Illumina

    • Reagent Cartridge

      • Supplier = Illumina

The version of AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing) master step name may be different depending on the version of IPP installed.

Automations

Register NovaSeq X Series Sequencing Run Started
  • Trigger Location = Step

  • Trigger Style = Automatic upon entry

Register NovaSeq X Series Sequencing Run Completed
  • Trigger Location = Step

  • Trigger Style = Automatic upon exit

Queue

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Current Cycle

    Text

    Read Only

    Current Read

    Text

    Read Only

    Flow Cell Expiration Date

    Text

    Read Only

    Flow Cell ID

    Text

    Read Only

    Flow Cell Lot Number

    Text

    Read Only

    Flow Cell Part Number

    Text

    Read Only

    Flow Cell Side

    Text

    Read Only

    Flow Cell Type

    Text

    Read Only

    Instrument Control Software Version

    Text

    Read Only

    Instrument ID

    Text

    Read Only

    Instrument Type

    Text

    Read Only

    Library Tube Strip Barcode

    Text

    Read Only

    Output Folder

    Text

    Read Only

    Run Name

    Text

    Read Only

    Run Status

    Text

    Read Only

    Sequencing Log

    Multiline Text

    Read Only

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      % Aligned R1

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Container

      % Aligned R2

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Container

      % Bases >=Q30 R1

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Container

      % Bases >=Q30 R2

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Container

      % Error Rate R1

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Container

      % Error Rate R2

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Container

      % Occupied

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Container

      % PF

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Container

      % Phasing R1

      Numeric

      Read Only

      Decimal Places Displayed = 3

      Container

      % Phasing R2

      Numeric

      Read Only

      Decimal Places Displayed = 3

      Container

      % Prephasing R1

      Numeric

      Read Only

      Decimal Places Displayed = 3

      Container

      % Prephasing R2

      Numeric

      Read Only

      Decimal Places Displayed = 3

      Container

      Container Name

      Built-in

      Container

      Intensity Cycle 1 R1

      Numeric

      Read Only

      Container

      Intensity Cycle 1 R2

      Numeric

      Read Only

      Container

      LIMS ID (Container)

      Built-in

      Container

      Reads PF

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Container

      Well

      Built-in

      Container

      Yield (Gb) R1

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Container

      Yield (Gb) R2

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Derived Sample

      Sample Name

      Built-in

      Measurement

      % Aligned R1

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Measurement

      % Aligned R2

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Measurement

      % Bases >=Q30 R1

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Measurement

      % Bases >=Q30 R2

      Numeric

      Read Only

      Measurement

      % Error Rate R1

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Measurement

      % Error Rate R2

      Numeric

      Read Only

      Measurement

      % Occupied

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Measurement

      % PF

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Measurement

      % Phasing R1

      Numeric

      Read Only

      Decimal Places Displayed = 3

      Measurement

      % Phasing R2

      Numeric

      Read Only

      Decimal Places Displayed = 3

      Measurement

      % Prephasing R1

      Numeric

      Read Only

      Decimal Places Displayed = 3

      Measurement

      % Prephasing R2

      Numeric

      Read Only

      Decimal Places Displayed = 3

      Measurement

      Intensity Cycle 1 R1

      Numeric

      Read Only

      Measurement

      Intensity Cycle 1 R2

      Numeric

      Read Only

      Measurement

      Reads PF

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Measurement

      Yield (Gb) R1

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Measurement

      Yield (Gb) R2

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Project

      Project Name

      Built-in

Step 6: AUTOMATED - Analysis Run (NovaSeq X Series Sequencing v2.0)

  • Master Step Name = AUTOMATED - Analysis Run (NovaSeq X Series Sequencing v2.0)

  • Step Type = Demultiplexing

  • Measurement Generation = Fixed, 1

  • Naming Convention = {SubmittedSampleName} {AppliedReagentLabels}

The version of AUTOMATED - Analysis Run (NovaSeq X Series Sequencing) master step name may be different depending on the version of IPP installed.

Queue

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Analysis Result Location

    Text

    Read Only

    Analysis Status

    Text

    Read Only

    Log

    Multiline Text

    Read Only

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

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