TruSeq Custom Amplicon v1.0

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Protocol 1: TruSeq Custom Amplicon (TSCA) v1.0

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Qubit QC (DNA) (TSCA v1.0)

Master Step Name = Qubit QC (DNA) v1.0
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName} Qubit

Automations

Assign QC flags (Qubit QC)

Trigger Location = Record Details
Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid1} -qcResult {compoundOutputFileLuid2}"

Set Next Step & Copy Concentration

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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:: ; input.::Concentration (ng/ul):: = output.::Concentration (ng/ul)::' -log {compoundOutputFileLuid0}"

Copy Concentration (ng/uL)

Trigger Location = Not Used

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 'input.::Concentration (ng/ul):: = output.::Concentration::' -log {compoundOutputFileLuid0}"

Qubit Copy Conc

Trigger Location = Not Used

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 'input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units:: ' \
        -log {compoundOutputFileLuid0}"

Queue/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
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Waiting
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  LIMS ID (Container)
  Built-in
  Project
  Project Name
  Built-in

Record Details

Group of Defaults

Concentration Thresholds

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Concentration (ng/ul)
Criteria 1 - Threshold Value = 10.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Concentration (ng/ul)
Criteria 2 - Threshold Value = 50.00

TSCA

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Concentration (ng/ul)
Criteria 1 - Threshold Value = 10.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Concentration (ng/ul)

Step Data

Group of Defaults = TSCA

Master Step Fields

Field Name

Field Type

Options

Additional Options and Dropdown Items

Criteria 1 - Operator

Text Dropdown

Presets

Criteria 1 - Source Data Field

Text Dropdown

Presets

Concentration (ng/ul)

Criteria 1 - Threshold Value

Numeric

Decimal Places Displayed = 2

Criteria 2 - Operator

Text Dropdown

Presets

Criteria 2 - Source Data Field

Text Dropdown

Presets

Concentration (ng/ul)

Criteria 2 - Threshold Value

Numeric

Decimal Places Displayed = 2

Step File Placeholders
- Qubit Result File - Manually uploaded
- QC Assignment Log File - Automatically attached
- QC Assignment Report - Automatically attached

Sample Table

Enable QC Flags = Yes
Sample Display Default = Expand
Well Sort Order = Row
File Column Options
- File Column Display = Hide
- File Attachment Method = Auto

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

Concentration (ng/ul)

Numeric

Decimal Places Displayed = 2

Derived Sample

Sample Name

Built-in

Measurement

Concentration (ng/ul)

Numeric

Decimal Places Displayed = 2

Project

Project Name

Built-in

Step 2: Normalize DNA 1 (TSCA v1.0)

Master Step Name = Normalize DNA 1 (TSCA v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSeq Custom Amplicon Low Input Kit, Box 2
  - Supplier = Illumina
  - Catalog Number = FC-134-2002; FC-134-2001
  - Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-custom-amplicon-low-input.html

ℹ️ The version of Normalized DNA 1 master step name may be different depending on the version of IPP installed.

Automations

Normalize DNA 1 Calculations

Trigger Location = Record Details
Trigger Style = Manual button

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 true -h false -exp 'output.::Sample Volume (ul):: = (step.::Target Normalization (ng/ul):: * step.::Final Volume (ul):: ) / input.::Concentration (ng/ul):: ; output.::Buffer Volume (ul):: = step.::Final Volume (ul):: - output.::Sample Volume (ul)::' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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}"

Queue/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
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Waiting
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  LIMS ID (Container)
  Built-in
  Project
  Project Name
  Built-in

Record Details

Step Data (Master Step Fields)

Field Name

Field Type

Options

Additional Options and Dropdown Items

Comment

Multiline Text

Final Volume (ul)

Numeric

Required Field

Default = 10
Decimal Places Displayed = 2

Target Normalization (ng/ul)

Numeric

Required Field

Decimal Places Displayed = 2

Step File Placeholders
- Log File - Automatically attached

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

Buffer Volume (ul)

Numeric

Decimal Places Displayed = 2

Derived Sample

Sample Name

Built-in

Derived Sample

Sample Volume (ul)

Numeric

Decimal Places Displayed = 2

Project

Project Name

Built-in

Step 3: Qubit QC (DNA) (TSCA v1.0)

Master Step Name = Qubit QC (DNA) v1.0
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName} Qubit

Automations

Assign QC flags (Qubit QC)

Trigger Location = Record Details
Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid1} -qcResult {compoundOutputFileLuid2}"

Set Next Step & Copy Concentration

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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:: ; input.::Concentration (ng/ul):: = output.::Concentration (ng/ul)::' -log {compoundOutputFileLuid0}"

Copy Concentration (ng/uL)

Trigger Location = Not Used

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 'input.::Concentration (ng/ul):: = output.::Concentration::' -log {compoundOutputFileLuid0}"

Qubit Copy Conc

Trigger Location = Not Used

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 'input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units:: ' \
        -log {compoundOutputFileLuid0}"

Queue/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
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Waiting
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  LIMS ID (Container)
  Built-in
  Project
  Project Name
  Built-in

Record Details

Group of Defaults

Concentration Thresholds

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Concentration (ng/ul)
Criteria 1 - Threshold Value = 10.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Concentration (ng/ul)
Criteria 2 - Threshold Value = 50.00

TSCA

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Concentration (ng/ul)
Criteria 1 - Threshold Value = 10.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Concentration (ng/ul)

Step Data

Group of Defaults = TSCA

Master Step Fields

Field Name

Field Type

Options

Additional Options and Dropdown Items

Criteria 1 - Operator

Text Dropdown

Presets

Criteria 1 - Source Data Field

Text Dropdown

Presets

Concentration (ng/ul)

Criteria 1 - Threshold Value

Numeric

Decimal Places Displayed = 2

Criteria 2 - Operator

Text Dropdown

Presets

Criteria 2 - Source Data Field

Text Dropdown

Presets

Concentration (ng/ul)

Criteria 2 - Threshold Value

Numeric

Decimal Places Displayed = 2

Step File Placeholders
- Qubit Result File - Manually uploaded
- QC Assignment Log File - Automatically attached
- QC Assignment Report - Automatically attached

Sample Table

Enable QC Flags = Yes
Sample Display Default = Expand
Well Sort Order = Row
File Column Options
- File Column Display = Hide
- File Attachment Method = Auto

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

Concentration (ng/ul)

Numeric

Decimal Places Displayed = 2

Derived Sample

Sample Name

Built-in

Measurement

Concentration (ng/ul)

Numeric

Decimal Places Displayed = 2

Project

Project Name

Built-in

Step 4: Normalize DNA 2 (TSCA v1.0)

Master Step Name = Normalize DNA 2 (TSCA v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSeq Custom Amplicon Low Input Kit, Box 2
  - Supplier = Illumina
  - Catalog Number = FC-134-2002; FC-134-2001
  - Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-custom-amplicon-low-input.html

ℹ️ The version of Normalized DNA 2 master step name may be different depending on the version of IPP installed.

Automations

Normalize DNA 2 Calculations

Trigger Location = Record Details
Trigger Style = Manual button

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 true -h false -exp 'output.::Sample Volume (ul):: = ((step.::Final Volume (ul):: * (step.::Desired Input DNA Amount (ng):: / step.::Final Volume (ul):: )) / input.::Concentration (ng/ul):: ) ; output.::Buffer Volume (ul):: = step.::Final Volume (ul):: - output.::Sample Volume (ul)::' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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}"

Queue/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
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Waiting
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  LIMS ID (Container)
  Built-in
  Project
  Project Name
  Built-in

Record Details

Step Data (Master Step Fields)

Field Name

Field Type

Options

Additional Options and Dropdown Items

Comment

Multiline Text

Desired Input DNA Amount (ng)

Numeric

Required Field

Decimal Places Displayed = 2

Final Volume (ul)

Numeric

Required Field

Default = 4
Decimal Places Displayed = 2

Step File Placeholders
- Log File - Automatically attached

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

Buffer Volume (ul)

Numeric

Decimal Places Displayed = 2

Derived Sample

Sample Name

Built-in

Derived Sample

Sample Volume (ul)

Numeric

Decimal Places Displayed = 2

Project

Project Name

Built-in

Step 5: Hybridize Oligo Pool (TSCA v1.0)

Master Step Name = Hybridize Oligo Pool (TSCA v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSeq Custom Amplicon Low Input Kit, Box 1
  - Supplier = Illumina
  - Catalog Number = FC-134-2002; FC-134-2001
  - Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-custom-amplicon-low-input.html
- TruSeq Custom Amplicon Low Input Kit, Box 2
  - Supplier = Illumina
  - Catalog Number = FC-134-2002; FC-134-2001
  - Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-custom-amplicon-low-input.html

ℹ️ The version of Hybridize Oligo Pool master step name may be different depending on the version of IPP installed.

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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}"

Queue/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
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Waiting
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  LIMS ID (Container)
  Built-in
  Project
  Project Name
  Built-in

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Row
Destination Containers
- 96 well plate

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
ELE Volume (ul) to add to ELB
Numeric Dropdown
Required Field
Presets
18
137
Decimal Places Displayed = 0
Step File Placeholders
- Log File - Automatically attached

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

Step 6: Remove Unbound Oligos (TSCA v1.0)

Master Step Name = Remove Unbound Oligos (TSCA v1.0.10)
Step Type = No Outputs
Reagent Kits