IGA Library Prep Automated v2.1

Overview

IGA Library Prep Automated v2.1 contains preset protocols that support the preparation of samples and libraries used for sequencing. These protocols can be used with the IGA NovaSeq Sequencing v2.1 workflow and NextSeq 1000/2000 v2.3 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

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Select Samples

• Master Step Name = Select Samples (IGA v2.1)
• Step Type = No Outputs

Automations

Validate Sample Attributes (IGA v2.1)

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

Sample Selection - Set Library prep method and Next steps (IGA v2.1)

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

Sample Selection - Route plated gDNA (IGA v2.1)

• 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
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in
    Project	Project Name	Built-in
    Submitted Sample	Illumina Universal Sample Identifier	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Submitted Sample	Sample Conc.	Numeric		Decimal Places Displayed = 2
    Submitted Sample	Units	Text

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 = 2.1.0.1
  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	Defaults = User tasks for this page: - Select Library Prep Method above - Select Next Steps

• Step File Placeholders

  • Set Library Prep Method Script Log - Automatically attached
• Sample Table (Table Columns - Global Fields)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Derived Sample	Sample Name	Built-in
  Submitted Sample	Library Prep Method	Text
  Submitted Sample	Sample Conc.	Numeric		Decimal Places Displayed = 2
  Submitted Sample	Submitted Sample Type	Text	Read Only
  Submitted Sample	Units	Text

Protocol 2: Sample Plating

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Plate Samples

• Master Step Name = Sample Plating (IGA v2.1)
• Step Type = Standard
• Derived Sample Generation = Variable
• Naming Convention = {InputItemlName}

Automations

Sample Plating & Extraction - Validate Single Sample Type and Library Prep Method (IGA v2.1)

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

Placement Reminder (IGA v2.1)

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

Sample Plating - Sample Placement SAM Plate Barcode Uniqueness Check (IGA v2.1)

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

Sample Plating - Set Transfer Volume & Create Liquid Handler Input File (IGA v2.1)

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

Sample Plating - Hamilton Output Plate Barcode Check, Store Instrument ID & Set Next Steps to Remove from Workflow before Custom Routing (IGA v2.1)

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

Sample Plating - Route samples (IGA v2.1)

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

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
    Submitted Sample	Library Prep Method	Text
    Submitted Sample	Sample Type	Text
    Submitted Sample	Sequencing Method	Text Dropdown	Custom Entries	Presets Single Read Paired End Read Indexed Single Read Indexed Paired End Read
    Submitted Sample	Submitted Sample Name	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Submitted Sample	Date Submitted	Built-in
    Submitted Sample	Sample Category	Text

Ice Bucket

• 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
  Submitted Sample	Library Prep Method	Text
  Submitted Sample	Sample Type	Text
  Submitted Sample	Sequencing Method	Text Dropdown	Custom Entries	Presets Single Read Paired End Read Indexed Single Read Indexed Paired End Read
  Submitted Sample	Submitted Sample Name	Built-in

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
  Liquid Handling Instrument ID	Text	Read Only
  Quick reference checklist: Sample Plating. i) pre Liquid Handler	Multiline Text	Read Only	Defaults = User tasks for this page: - Select blue 'Run' button - Download Liquid Handler Input File
  Quick reference checklist: Sample Plating. ii) post Liquid Handler	Multiline Text	Read Only	Defaults = User tasks continued: - Upload resulting Liquid Handler Output File - Select Next Steps
  Step Sample Type	Text	Read Only

• Step File Placeholders

  • Liquid Handler Input File - Automatically attached
  • Script Log File (Aggregated) - Automatically attached
  • Liquid Handler Output File - Manually uploaded
• Sample Table (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
  Submitted Sample	Sample Type	Text
  Submitted Sample	Submitted Sample Labware Type	Text

Protocol 3: Blood Extraction

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: DNA Extraction - Blood

• Master Step Name = DNA Extraction - Blood (IGA v2.1)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {InputItemName}

Automations

Sample Plating & Extraction - Validate Single Sample Type and Library Prep Method (IGA v2.1)

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

Extraction - Sample Placement EDP Plate Barcode Uniqueness Check (IGA v2.1)

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

Extraction - Count Samples & Create LH Input File (IGA v2.1)

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

Extraction - Check LH Output File Barcode & Parse Reagent Info & Check for Missing Barcodes & Set Next Steps to Remove from Workflow (IGA v2.1)

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

Extraction - Routing (IGA v2.1)

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

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
  Submitted Sample	Library Prep Method	Text
  Submitted Sample	Sample Type	Text
  Submitted Sample	Sequencing Method	Text Dropdown	Custom Entries	Presets Single Read Paired End Read Indexed Single Read Indexed Paired End Read
  Submitted Sample	Submitted Sample Name	Built-in

Ice Bucket

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

• Step File Placeholders

  • Liquid Handling Robot (Hamilton) Input File - Automatically attached
  • Script Log File (Aggregated) - Automatically attached
  • Liquid Handling Robot Output File - Manually uploaded
• Sample Table (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
  Submitted Sample	Library Prep Method	Text

Protocol 4: Saliva Extraction

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: DNA Extraction - Saliva

• Master Step Name = DNA Extraction - Blood (IGA v2.1)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {InputItemName}

Automations

Sample Plating & Extraction - Validate Single Sample Type and Library Prep Method (IGA v2.1)

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

Extraction - Sample Placement EDP Plate Barcode Uniqueness Check (IGA v2.1)

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

Extraction - Count Samples & Create LH Input File (IGA v2.1)

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

Extraction - Check LH Output File Barcode & Parse Reagent Info & Check for Missing Barcodes & Set Next Steps to Remove from Workflow (IGA v2.1)

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

Extraction - Routing (IGA v2.1)

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

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
  Submitted Sample	Library Prep Method	Text
  Submitted Sample	Sample Type	Text
  Submitted Sample	Sequencing Method	Text Dropdown	Custom Entries	Presets Single Read Paired End Read Indexed Single Read Indexed Paired End Read
  Submitted Sample	Submitted Sample Name	Built-in

Ice Bucket

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

• Step File Placeholders

  • Liquid Handling Robot (Hamilton) Input File - Automatically attached
  • Script Log File (Aggregated) - Automatically attached
  • Liquid Handling Robot Output File - Manually uploaded
• Sample Table (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
  Submitted Sample	Library Prep Method	Text

Protocol 5: Illumina DNA PCR-Free

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: DNA Batching PCR-Free

• Master Step Name = DNA Batching NFPF (IGA v2.1)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {InputItemName}_DNA

Automations

DNA Batching PF - Set Final Volume and Validate Sample Type Combination (IGA v2.1)

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

Placement Reminder (IGA v2.1)

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

DNA Batching - Sample Placement DNA Plate Barcode Uniqueness Check (IGA v2.1)

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

DNA Batching PF - Generate LH Input File (IGA v2.1)

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

DNA Batching - Check LH Output File Barcode, Store Instrument ID, Set Next Steps to Advance (IGA v2.1)

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

Register Step Completed (IGA v2.1)

• 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