TruSeq Custom Amplicon v1.0

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

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

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

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
- 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

The version of Remove Unbound Oligos 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

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
60% EtOH Prep Date
Date
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 7: Extend and Ligate Bound Oligos (TSCA v1.0)

Master Step Name = Extend and Ligate Bound Oligos (TSCA v1.0.10)
Step Type = No Outputs
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

The version of Extend and Ligate Bound Oligos 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

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
EDP Volume (ul)
Numeric
Required Field
Custom Entries
Presets
1.1
17.6
53
106
EMM Volume (ul)
Numeric
Required Field
Custom Entries
Presets
21
334
1003
2006
Thermal Cycler Program
Text
Default = EXT_LIG
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 8: Amplify Libraries (TSCA v1.0)

Master Step Name = Amplification with Labels v2.0
Step Type = Add Labels
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

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}"

Copy to Output

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 'output.::RNA Sample Type:: = input.::RNA Sample Type::' -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
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

Add Labels

Label Groups
- TruSeq Custom Amplicon (TSCA) Low Input

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Number of PCR Cycles
Text Dropdown
Custom Entries
Presets
32
29
28
27
25
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 9: Clean Up Libraries (TSCA v1.0)

Master Step Name = Clean Up v2.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
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 3
  - 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

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

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
80% EtOH Prep Date
Date
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 10: Bioanalyzer QC (Library Validation) (TSCA v1.0)

Master Step Name = Bioanalyzer QC (Library Validation) v2.0
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName} Bioanalyzer

Automations

Generate Bioanalyzer Input file

Trigger Location = Record Details
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar script:driver_file_generator -i {processURI:v2} -u {username} -p {password} -t /opt/gls/clarity/extensions/ngs-common/v5/EPP/conf/readonly/bioA_driver_file_template.csv -o {compoundOutputFileLuid0}.csv -l {compoundOutputFileLuid1}  && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar script:addBlankLines -i {stepURI:v2} -u {username} -p {password} -f {compoundOutputFileLuid0}.csv -l {compoundOutputFileLuid1} -sep COMMA -b ',False,' -h 1 -c LIMSID -pre 'Sample '"

Parse Bioanalyzer XML, Copy nM and Assign QC flags

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:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' && /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 'if (output.::Conc. Units::.contains(::pg::)) {output.::Molarity (nM):: = output.::Region 1 Molarity:: / 1000} else {output.::Molarity (nM):: = output.::Region 1 Molarity::} ; (input.::Molarity (nM):: = output.::Molarity (nM)::) ' -log {compoundOutputFileLuid8} && /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 {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"

Set Next Step - Output PASS/FAIL

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 true -h false -excludeControls true -exp 'if (output.QC == true) { nextStep = ::ADVANCE:: } else { nextStep = ::ESCALATE:: }' -log {compoundOutputFileLuid0}"

Parse Bioanalyzer XML and assign QC flags

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 {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"

Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations

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 {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7} && /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.::Concentration:: = output.::Region 1 Conc.:: ; input.::Concentration:: = output.::Concentration:: ; output.::Conc. Units:: = ::ng/ul:: ; input.::Conc. Units:: = output.::Conc. Units::' -log {compoundOutputFileLuid8}"

Parse Bioanalyzer XML, Calculate nM and assign QC flags

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 {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' && /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.::Concentration:: = output.::Region 1 Conc.:: ; output.::Molarity (nM):: = (output.::Concentration:: * 1000000) / (660 * output.::Region 1 Average Size - bp::) ; input.::Molarity (nM):: = output.::Molarity (nM):: ; output.::Conc. Units:: = ::ng/ul::' -log {compoundOutputFileLuid8} && /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 {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"

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
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
- BioAnalyzer DNA High Sensitivity Chip
- BioAnalyzer DNA 1000 Chip

Record Details

Group of Defaults

Nextera DNA Flex Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 150.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 1,500.00

Nextera Mate Pair Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 400.00

Nextera XT DNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 250.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 1,000.00

NRCC Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 350.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 1,000.00

TruSeq ChIP-Seq Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 400.00

TruSeq Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 150.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 1,000.00

TruSeq Methyl Capture EPIC Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 300.00

TruSeq Rapid Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 500.00

TruSeq RNA Access Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 320.00

TruSeq RNA Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 320.00

TruSeq Small RNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 100.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 200.00

TruSeq Stranded mRNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 250.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 275.00

TruSeq Stranded Total RNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 250.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 275.00

TruSeq Targeted RNA Expression Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 100.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 300.00

TruSight Myeloid Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Size - bp
Criteria 2 - Threshold Value = 400.00

TruSight RNA Fusion Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 160.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Size - bp
Criteria 2 - Threshold Value = 700.00

TSCA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 300.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Size - bp
Criteria 2 - Threshold Value = 400.00

Step Data
- Group of Defaults = TSCA Library Validation
- Master Step Fields
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Criteria 1 - Operator
  Text Dropdown
  Custom Entries
  Presets
  >=
  <=
  =
  !=
  Criteria 1 - Source Data Field
  Text Dropdown
  Presets
  Concentration
  Conc. Units
  Number of Peaks found
  Peak 1 Size - bp
  Peak 1 Conc.
  Peak 1 Molarity
  Peak 2 Size - bp
  Peak 2 Conc.
  Peak 2 Molarity
  Peak 3 Size - bp
  Peak 3 Conc.
  Peak 3 Molarity
  Peak 4 Size - bp
  Peak 4 Conc.
  Peak 4 Molarity
  Peak 5 Size - bp
  Peak 5 Conc.
  Peak 5 Molarity
  Number of Regions found
  Region 1 Average Size - bp
  Region 1 Conc.
  Region 1 Molarity
  Region 2 Average Size - bp
  Region 2 Conc.
  Region 2 Molarity
  Region 3 Average Size - bp
  Region 3 Conc.
  Region 3 Molarity
  Region 4 Average Size - bp
  Region 4 Conc.
  Region 4 Molarity
  Region 5 Average Size - bp
  Region 5 Conc.
  Region 5 Molarity
  Criteria 1 - Threshold Value
  Numeric
  Decimal Places Displayed = 2
  Criteria 2 - Operator
  Text Dropdown
  Custom Entries
  Presets
  >=
  <=
  =
  !=
  Criteria 2 - Source Data Field
  Text Dropdown
  Presets
  Concentration
  Conc. Units
  Number of Peaks found
  Peak 1 Size - bp
  Peak 1 Conc.
  Peak 1 Molarity
  Peak 2 Size - bp
  Peak 2 Conc.
  Peak 2 Molarity
  Peak 3 Size - bp
  Peak 3 Conc.
  Peak 3 Molarity
  Peak 4 Size - bp
  Peak 4 Conc.
  Peak 4 Molarity
  Peak 5 Size - bp
  Peak 5 Conc.
  Peak 5 Molarity
  Number of Regions found
  Region 1 Average Size - bp
  Region 1 Conc.
  Region 1 Molarity
  Region 2 Average Size - bp
  Region 2 Conc.
  Region 2 Molarity
  Region 3 Average Size - bp
  Region 3 Conc.
  Region 3 Molarity
  Region 4 Average Size - bp
  Region 4 Conc.
  Region 4 Molarity
  Region 5 Average Size - bp
  Region 5 Conc.
  Region 5 Molarity
  Criteria 2 - Threshold Value
  Numeric
  Decimal Places Displayed = 2
  Use strict matching for Bioanalyzer results
  Toggle Switch
  Default = None Set
Step File Placeholders
- Bioanalyzer Input File - Automatically attached
- Bioanalyzer Input File Generation Log File - Automatically attached
- Bioanalyzer XML Result File (required) - Manually uploaded
- Result File (optional) - Manually uploaded
- PDF Summary File (optional) - Manually uploaded
- Bioanalyzer XML Parsing Log File - Automatically attached
- QC Assignment Log File - Automatically attached
- QC Assignment Report - Automatically attached
Sample Table
- Enable QC Flags = Yes
- Sample Display Default = Expand
- Well Sort Order = Column
- 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
  Derived Sample
  Molarity (nM)
  Numeric
  Decimal Places Displayed = 2
  Derived Sample
  Sample Name
  Built-in
  Measurement
  BA Sample Name
  Text
  Measurement
  Concentration
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Conc. Units
  Text
  Measurement
  Molarity (nM)
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Number of Peaks found
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Number of Regions found
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Peak 1 Conc.
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Peak 1 Molarity
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Peak 1 Size - bp
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Peak 2 Conc.
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Peak 2 Molarity
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Peak 2 Size - bp
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Peak 3 Conc.
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Peak 3 Molarity
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Peak 3 Size - bp
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Peak 4 Conc.
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Peak 4 Molarity
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Peak 4 Size - bp
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Peak 5 Conc.
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Peak 5 Molarity
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Peak 5 Size - bp
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Region 1 Average Size - bp
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Region 1 Conc.
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Region 1 Molarity
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Region 2 Average Size - bp
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Region 2 Conc.
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Region 2 Molarity
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Region 3 Average Size - bp
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Region 3 Conc.
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Region 3 Molarity
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Region 4 Average Size - bp
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Region 4 Conc.
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Region 4 Molarity
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Region 5 Average Size - bp
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Region 5 Conc.
  Numeric
  Decimal Places Displayed = 2
  Measurement
  Region 5 Molarity
  Numeric
  Decimal Places Displayed = 2

Step 11: Normalize Libraries (TSCA v1.0)

Master Step Name = Normalize Libraries 3 v2.0.10
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
- TruSeq Custom Amplicon Low Input Kit, Box 3
  - 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

The version of Normalized Libraries 3 master step name may be different depending on the version of IPP installed.

Automations

Set Next Step - Remove

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 = ::REMOVE::' -log {compoundOutputFileLuid0}"

Routing script - Normalize Libraries

Trigger Location = Step
Trigger Style = Automatic upon exit

bash -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'MiSeq' \
--WORKFLOW 'MiSeq Sequencing v3.2' \
--STEP 'Library Pooling (MiSeq v3.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NextSeq' \
--WORKFLOW 'NextSeq 500/550 Sequencing v1.2' \
--STEP 'Library Pooling (NextSeq 500/550 v1.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeq 2.0' \
--WORKFLOW 'NovaSeq 6000 v2.3' \
--STEP 'Define Run Format (NovaSeq 6000 v2.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeq 3.0' \
--WORKFLOW 'NovaSeq 6000 v3.8' \
--STEP 'Define Run Format (NovaSeq 6000 v3.8)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeqDx' \
--WORKFLOW 'NovaSeqDx v1.2' \
--STEP 'Define Run Format (NovaSeqDx v1.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NextSeq 1000/2000' \
--WORKFLOW 'NextSeq 1000/2000 Sequencing v2.4' \
--STEP 'Library Pooling and Dilution (NextSeq 1000/2000 Sequencing v2.4)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeq X Series' \
--WORKFLOW 'NovaSeq X Series v1.1' \
--STEP 'Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NextSeq 1000/2000 On-Prem' \
--WORKFLOW 'NextSeq 1000/2000 On-Prem Sequencing v1.0' \
--STEP 'Library Pooling and Dilution (NextSeq 1000/2000 On-Prem Sequencing v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ The field name, workflow version and step version for the Sequencing Instrument may vary depending on the version of the IPP.

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
0.1 N NaOH Prep Date
Date
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
  Normalized Molarity (nM)
  Numeric
  Decimal Places Displayed = 2
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Sequencing Instrument
  Text Dropdown
  Required Field
  Presets
  MiSeq
  NextSeq
  NextSeq 1000/2000
  NextSeq 1000/2000 On-Prem
  NovaSeq 2.0
  NovaSeq 3.0
  NovaSeq X Series
  NovaSeqDx
  Project
  Project Name
  Built-in
  ℹ The preset options for Derived Sample Sequencing Instrument may vary depending on the version of the IPP.

PreviousTruSeq ChIP-Seq v1.0 NextTruSeq DNA Exome v2.0

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

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

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

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

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

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

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

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

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

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

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagPlacement = Enabled

hashtagRecord Details

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

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

hashtagStep 7: Extend and Ligate Bound Oligos (TSCA v1.0)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

hashtagStep 8: Amplify Libraries (TSCA v1.0)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagAdd Labels

hashtagRecord Details

hashtagStep 9: Clean Up Libraries (TSCA v1.0)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

hashtagStep 10: Bioanalyzer QC (Library Validation) (TSCA v1.0)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagPlacement = Enabled

hashtagRecord Details

hashtagStep 11: Normalize Libraries (TSCA v1.0)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

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

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

Automations

Queue/Ice Bucket

Record Details

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

Automations

Queue/Ice Bucket

Record Details

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

Automations

Queue/Ice Bucket

Record Details

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

Automations

Queue/Ice Bucket

Record Details

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

Automations

Queue/Ice Bucket

Placement = Enabled

Record Details

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

Automations

Queue/Ice Bucket

Record Details

Step 7: Extend and Ligate Bound Oligos (TSCA v1.0)

Automations

Queue/Ice Bucket

Record Details

Step 8: Amplify Libraries (TSCA v1.0)

Automations

Queue/Ice Bucket

Add Labels

Record Details

Step 9: Clean Up Libraries (TSCA v1.0)

Automations

Queue/Ice Bucket

Record Details

Step 10: Bioanalyzer QC (Library Validation) (TSCA v1.0)

Automations

Queue/Ice Bucket

Placement = Enabled

Record Details

Step 11: Normalize Libraries (TSCA v1.0)

Automations

Queue/Ice Bucket

Record Details