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Equalizer v1.1

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Overview

The Equalizer Workflow AmpliSeq for Illumina Immune Repertoire Panel v1.1 is part of the AmpliSeq for Illumina Immune Repertoire Panel protocols that include the following functionality:

  • Preconfigured AmpliSeq for Illumina Immune Repertoire Panel protocol that supports the preparation of up to 96 uniquely indexed libraries of genomic DNA or total RNA using the AmpliSeq for Illumina workflow.

  • Automated calculation of sample and buffer volumes.

  • Automated calculation or display of reagents at every step in the protocol.

  • Automatic step transition when required.

  • Automatic placement of samples when necessary.

  • Automated assignment of QC Pass/Fail, based on user-selected threshold values.

  • A routing script that allows sequencing of libraries using any Illumina sequencing instrument.

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Protocol 1: Equalizer Workflow (AmpliSeq for Illumina Immune Repertoire Panel v1.1)

Protocol Type = Library Prep

Next Steps Configuration

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Step 1: Clean Up Library (AmpliSeq for Illumina Immune Repertoire Panel v1.1)

  • Master Step Name = Clean Up Library (AmpliSeq for Illumina v1.1)

  • Step Type = No Outputs

  • Reagent Kits

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Automations

chevron-rightSet Next Step - Advancehashtag
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

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Record Details

  • Step Data (Master Step Fields)

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Step 2: Amplify Library (AmpliSeq for Illumina Immune Repertoire Panel v1.1)

  • Master Step Name = Amplify Library (AmpliSeq for Illumina v1.1)

  • Step Type = No Outputs

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Automations

chevron-rightCount Samples and Calculate Master Mixhashtag
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon entry

chevron-rightSet Next Step - Advancehashtag
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

chevron-rightCalculate Total Samples and Calculate Master Mixhashtag
  • Trigger Location = Not Used

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Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

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Record Details

Group of Defaults

chevron-rightAmpliSeq for CHS V2hashtag
  • Thermal Cycler Program = AMP

chevron-rightEqualizer Workflowhashtag
  • Thermal Cycler Program = EQUAL

chevron-rightStandard Workflowhashtag
  • Thermal Cycler Program = AMP_7

  • Step Data

    • Group of Defaults = Equalizer Workflow

    • Master Step Fields

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Step 3: Perform Capture and Clean Up (AmpliSeq for Illumina Immune Repertoire Panel v1.1)

  • Master Step Name = Perform Capture and Clean Up (AmpliSeq for Illumina v1.1)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

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Automations

chevron-rightSet Next Step - Advancehashtag
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

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Record Details

  • Step File Placeholders

    • Log - Automatically attached

  • Sample Table

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Step 4: Elute Library (AmpliSeq for Illumina Immune Repertoire Panel v1.1)

  • Master Step Name = Elute Library (AmpliSeq for Illumina v1.1)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

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Automations

chevron-rightSet Next Step - Advancehashtag
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

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Placement = Enabled

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

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Record Details

  • Step Data (Master Step Fields)

Agencourt AMPure XP Beads
  • Supplier = Thermo

  • Catalog Number = NC9959336; NC9933872

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

Step File Placeholders
  • Log - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

  • 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

    Options

    Additional Options and Dropdown Items

    1X Lib AMP Mix (uL)

    Numeric

    Decimal Places Displayed = 2

    10X Library Amp Primers (uL)

    Numeric

    Decimal Places Displayed = 2

    Thermal Cycler Program

    Text Dropdown

    Custom Entries

    Presets

    • AMP_7

    • EQUAL

    • AMP

    Total Samples

    Numeric

    Default = 0

  • Step File Placeholders

    • Log - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

  • Naming Convention = {InputItemName}
  • Reagent Kits

    • AmpliSeq Library Equalizer for Illumina

      • Supplier = Illumina

      • Website =

  • 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

    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

  • Naming Convention = {InputItemName}
  • Reagent Kits

    • AmpliSeq Library PLUS for Illumina

      • Supplier = Illumina

      • Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103

      • Website =

  • 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

    Placement Pattern = Row
  • Destination Containers

    • 96 well plate

  • Step File Placeholders
    • Log - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Row

    • Table Columns - Global Fields

  • Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    70% EtOH Prep Date

    Date

    Field Name

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Thermal Cycler Program

    Text

    Default = ELUTE

    Field Type

    bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
          script:evaluateDynamicExpression \
          -t false \
          -h false \
          -exp 'nextStep = ::ADVANCE::' \
          -log {compoundOutputFileLuid0}"
    bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
          script:evaluateDynamicExpression \
          -t false \
          -h false \
          -exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
          -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
          script:evaluateDynamicExpression \
          -t false \
          -h false \
          -exp 'step.::1X Lib AMP Mix (uL):: = step.::Total Samples:: * 1.1 * 45 ; \
    step.::10X Library Amp Primers (uL):: = step.::Total Samples:: * 1.1 * 5' \
          -log {compoundOutputFileLuid0}"
    bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
          script:evaluateDynamicExpression \
          -t false \
          -h false \
          -exp 'nextStep = ::ADVANCE::' \
          -log {compoundOutputFileLuid0}"
    bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \ -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'step.::1X Lib Amp Mix:: = step.::Total Samples:: * 1.1 * 45 ; \ step.::10X Library Amp Primers:: = step.::Total Samples:: * 1.1 * 5' \ -log {compoundOutputFileLuid0}"
    bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
          script:evaluateDynamicExpression \
          -t false \
          -h false \
          -exp 'nextStep = ::ADVANCE::' \
          -log {compoundOutputFileLuid0}"
    bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
          script:evaluateDynamicExpression \
          -t false \
          -h false \
          -exp 'nextStep = ::ADVANCE::' \
          -log {compoundOutputFileLuid0}"

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Project

    Project Name

    Built-in

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Project

    Project Name

    Built-in

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Project

    Project Name

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

    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

    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

    LIMS ID (Container)

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Project

    Project Name

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

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    www.illumina.comarrow-up-right

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