IGA Library Prep Automated v3.0

Overview

IGA Library Prep Automated v3.0 contains preset protocols that support the preparation of samples and libraries used for sequencing. These protocols can be used with the NovaSeq X Series Sequencing v2.0 workflow (which is installed separately). The protocols provide the following functions:

• File-based integration with the Hamilton robots that are used for liquid handling steps.
• Automated calculation of sample and buffer volumes.
• Automated calculation or display of reagents.
• When required, automatic step transition.

Protocol 1: Sample Selection (IGA v3.0)

Protocol Type = Sample Prep

Next Steps Configuration

• Step(s):

  • 1: Select Samples (IGA v3.0)

    • Assign Next Step = Automatic

Step 1: Select Samples (IGA v3.0)

• Master Step Name = Sample Selection (IGA v3.0)
• Step Type = No Outputs

The version of Sample Selection (IGA) master step name may be different depending on the version of IPP installed.

Automations

Validate Sample Attributes (IGA v3.0)

• Trigger Location = Step
• Trigger Style = Automatic upon entry

Sample Selection - Set Library prep method and Next steps (IGA v3.0)

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

Sample Selection - Route plated gDNA (IGA v3.0)

• Trigger Location = Step
• 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.

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
  IGA WF Build Version	Text	Read Only	Default = 3.0.0.5-SNAPSHOT
  Library Prep Method	Text Dropdown	Required Field	Presets Illumina DNA PCR-Free Illumina DNA with Enrichment
  Quick reference checklist: Sample Selection	Multiline Text	Read Only	Default = User tasks for this page: - Select Library Prep Method above - Select Next Steps

• Sample Table

  • Sample Display Default = Collapse
  • Well Sort Order = Column
  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	Sample Name	Built-in

Protocol 2: Sample Plating (IGA v3.0)

Protocol Type = Sample Prep

Next Steps Configuration

• Step(s):

  • 1: Plate Samples (IGA v3.0)

    • Assign Next Step = Automatic

Step 1: Plate Samples (IGA v3.0)

• Master Step Name = Sample Plating (IGA v3.0)
• Step Type = Standard
• Derived Sample Generation = Variable, 3
• Naming Convention = {InputItemName}

The version of Sample Plating (IGA) master step name may be different depending on the version of IPP installed.

Automations

Sample Plating & Extraction - Validate Single Sample Type and Library Prep Method (IGA v3.0)

• Trigger Location = Step
• Trigger Style = Automatic upon entry

Placement Reminder (IGA v3.0)

• Trigger Location = Placement
• Trigger Style = Automatic upon entry

Sample Plating - Sample Placement SAM Plate Barcode Uniqueness Check (IGA v3.0)

• Trigger Location = Placement
• Trigger Style = Automatic upon exit

Sample Plating - Set Transfer Volume & Create LHR Input File (IGA v3.0)

• Trigger Location = Record Details
• Trigger Style = Manual button

Sample Plating - LHR Output Plate Barcode Check, Store Instrument ID & Set Next Steps to Remove from Workflow before Custom Routing (IGA v3.0)

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

Sample Plating - Route samples (IGA v3.0)

• Trigger Location = Step
• 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.

Queue

• Defaults

  • Sample Grouping = Group by Projects
  • Well Sort Order = Column
• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Derived Sample	Waiting	Built-in

Ice Bucket

• Defaults

  • Sample Grouping = Group by Projects
  • Well Sort Order = Column

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Projects
  • Well Sort Order = Column
  • Placement Pattern = Column
• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  LHR Instrument ID	Text	Read Only
  Quick reference checklist: Sample Plating. i) pre LHR	Multiline Text	Read Only	Default = User tasks for this page: - Select blue 'Run' button - Download LHR Input File
  Quick reference checklist: Sample Plating. ii) post LHR	Multiline Text	Read Only	Default = User tasks continued: - Upload resulting LHR Output File - Select Next Steps
  Step Sample Type	Text	Read Only

• Sample Table

  • Sample Display Default = Expand
  • Well Sort Order = Column
  • 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
    Derived Sample	Submitted Sample Type	Text	Read Only
    Derived Sample	Transfer Volume (ul)	Numeric

Protocol 3: Blood Extraction (IGA v3.0)

Protocol Type = Sample Prep

Next Steps Configuration

• Step(s):

  • 1: DNA Extraction - Blood (IGA v3.0)

    • Assign Next Step = Automatic

Step 1: DNA Extraction - Blood (IGA v3.0)

• Master Step Name = DNA Extraction - Blood (IGA v3.0)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {InputItemName}

The version of DNA Extraction - Blood (IGA) master step name may be different depending on the version of IPP installed.

Automations

Sample Plating & Extraction - Validate Single Sample Type and Library Prep Method (IGA v3.0)

• Trigger Location = Step
• Trigger Style = Automatic upon entry

Extraction - Sample Placement EDP Plate Barcode Uniqueness Check (IGA v3.0)

• Trigger Location = Placement
• Trigger Style = Automatic upon exit

Extraction - Count Samples & Create LHR Input File (IGA v3.0)

• Trigger Location = Record Details
• Trigger Style = Automatic upon entry

Extraction - Check LHR Output File Barcode & Parse Reagent Info & Check for Missing Barcodes & Set Next Steps to Remove from Workflow (IGA v3.0)

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

Extraction - Routing (IGA v3.0)

• Trigger Location = Step
• 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.

Queue

• Defaults

  • Sample Grouping = Group by Containers
  • Well Sort Order = Column
• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Derived Sample	Waiting	Built-in

Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers
  • Well Sort Order = Column

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers
  • Well Sort Order = Column
  • Placement Pattern = Column
• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Ethanol	Text
  ITB	Text
  LHR Instrument ID	Text	Read Only
  MLB	Text
  ProK	Text
  Quick reference checklist: DNA Extraction - Blood. i) pre LHR	Multiline Text	Read Only	Default = User tasks for this page: - Download LHR Input File - Enter reagent lots for MLB and ProK (not scanned by LHR as loaded as a mastermix)
  Quick reference checklist: DNA Extraction - Blood. ii) post LHR	Multiline Text	Read Only	Default = User tasks continued: - After running Extraction on the liquid handler, upload the resulting LHR Output File - Select Next Steps (RSB, ITB and Ethanol lots will populate automatically on the next screen)
  RSB	Text
  Sample Count	Numeric	Read Only	Default = 0
  Step Sample Type	Text	Read Only

• Sample Table

  • Sample Display Default = Collapse
  • Well Sort Order = Column
  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container	Built-in
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Submitted Sample Type	Text	Read Only
    Project	Project Name	Built-in

Protocol 4: Saliva Extraction (IGA v3.0)

Protocol Type = Sample Prep

Next Steps Configuration

• Step(s):

  • 1: DNA Extraction - Saliva (IGA v3.0)

    • Assign Next Step = Automatic

Step 1: DNA Extraction - Saliva (IGA v3.0)

• Master Step Name = DNA Extraction - Saliva (IGA v3.0)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {InputItemName}

The version of DNA Extraction - Saliva (IGA) master step name may be different depending on the version of IPP installed.

Automations

Sample Plating & Extraction - Validate Single Sample Type and Library Prep Method (IGA v3.0)

• Trigger Location = Step
• Trigger Style = Automatic upon entry

Extraction - Sample Placement EDP Plate Barcode Uniqueness Check (IGA v3.0)

• Trigger Location = Placement
• Trigger Style = Automatic upon exit

Extraction - Count Samples & Create LHR Input File (IGA v3.0)

• Trigger Location = Record Details
• Trigger Style = Automatic upon entry

Extraction - Check LHR Output File Barcode & Parse Reagent Info & Check for Missing Barcodes & Set Next Steps to Remove from Workflow (IGA v3.0)

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

Extraction - Routing (IGA v3.0)

• Trigger Location = Step
• 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.

Queue

• Defaults

  • Sample Grouping = Group by Containers
  • Well Sort Order = Column
• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Derived Sample	Waiting	Built-in

Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers
  • Well Sort Order = Column

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers
  • Well Sort Order = Column
  • Placement Pattern = Column
• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Ethanol	Text
  ITB	Text
  LHR Instrument ID	Text
  MLB	Text
  ProK	Text
  Quick reference checklist: DNA Extraction - Saliva. i) pre LHR	Multiline Text	Read Only	Default = User tasks for this page: - Download LHR Input File - Enter reagent lots for MLK and ProK (not scanned by LHR as loaded as a mastermix)
  Quick reference checklist: DNA Extraction - Saliva. ii) post LHR	Multiline Text	Read Only	Default = User tasks continued: - After running Extraction on the liquid handler, upload the resulting LHR Output File - Select Next Steps (RSB, ITB and Ethanol lots will populate automatically on the next screen)
  RSB	Text
  Sample Count	Numeric	Read Only	Default = 0
  Step Sample Type	Text	Read Only

• 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	Built-in
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Submitted Sample Type	Text	Read Only
    Project	Project Name	Built-in

Protocol 5: Illumina DNA PCR-Free (IGA v3.0)

Protocol Type = Library Prep

Next Steps Configuration

• Step(s):

  • 1: DNA Batching PCR-Free (IGA v3.0)

    • Start Next Step = Manual
    • Assign Next Step = Manual
  • 2: Indexing Planning PCR-Free (IGA v3.0)

    • Start Next Step = Manual
    • Assign Next Step = Manual
  • 3: Library Prep - Indexing PCR-Free (IGA v3.0)

    • Assign Next Step = Automatic

Step	To Step 1	To Step 2	To Step 3
1		✓	❌
2			✓
3

Step 1: DNA Batching PCR-Free (IGA v3.0)

• Master Step Name = DNA Batching NFPF (IGA v3.0)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {InputItemName}_DNA

The version of DNA Batching NFPF (IGA) master step name may be different depending on the version of IPP installed.

Automations

DNA Batching PF - Set Final Volume and Validate Sample Type Combination (IGA v3.0)

• Trigger Location = Step
• Trigger Style = Automatic upon entry

Placement Reminder (IGA v3.0)

• Trigger Location = Placement
• Trigger Style = Automatic upon entry

DNA Batching - Sample Placement DNA Plate Barcode Uniqueness Check (IGA v3.0)

• Trigger Location = Placement
• Trigger Style = Automatic upon exit

DNA Batching PF - Generate LHR Input File (IGA v3.0)

• Trigger Location = Record Details
• Trigger Style = Manual button

DNA Batching - Check LHR Output File Barcode, Store Instrument ID, Set Next Steps to Advance (IGA v3.0)

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

Register Step Completed (IGA v3.0)

• 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

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers
  • Well Sort Order = Column
  • Placement Pattern = Column
• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Batching Well Volume (uL)	Numeric	Required Field	Default = 40
  DNA (ng) required for tagmentation	Numeric	Required Field	Default = 350
  LHR Instrument ID	Text	Read Only
  Notes:	Multiline Text	Read Only	Default = - DNA (ng) required for tagmentation is 300-2000 ng. - A fixed 25uL is aliquoted from the total volume of 40uL (default) to carry out Library Prep and subsequent steps.
  Quick reference checklist: DNA Batching IDPF. i) pre LHR	Multiline Text	Read Only	Default = User tasks for this page: - For gDNA samples, enter library prep Input Amount (ng). NB: this field is ignored for samples which arrived as raw blood or saliva, as a set volume is transferred - 'Run' DNA Batching PF automation, and download resulting 'LHR Input File'
  Quick reference checklist: DNA Batching IDPF. ii) post LHR	Multiline Text	Read Only	Default = User tasks continued: - Upload resulting 'LHR Output File' - Select 'Next Steps'

• Sample Table

  • Sample Display Default = Collapse
  • Well Sort Order = Column
  • 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	Diluent Volume (uL)	Numeric		Decimal Places Displayed = 1
    Derived Sample	Initial Input DNA (ng)	Numeric
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample Needed (uL)	Numeric		Decimal Places Displayed = 1
    Derived Sample	Warnings	Text	Read Only
    Project	Project Name	Built-in

Step 2: Indexing Planning PCR-Free (IGA v3.0)

• Master Step Name = Indexing Planning (IGA v3.0)
• Step Type = No Outputs

The version of Indexing Planning (IGA) master step name may be different depending on the version of IPP installed.

Automations

Register Step Started (IGA v3.0)

• Trigger Location = Step
• Trigger Style = Automatic upon entry

Indexing Planning - Validate and Check for Duplicates of Index Plate Barcode, Validate Indexing Offset, and Set Next Steps (IGA v3.0)

• 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 (IGA v3.0)

• Trigger Location = Step
• Trigger Style = Automatic upon exit