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TruSeq Nano DNA v1.0

Overview

The TruSeq Nano DNA includes the following functionality:

  • Preconfigured TruSeq Nano DNA protocol that explains how to prepare up to 96 uniquely indexed paired-end libraries of genomic DNA (gDNA) using Illumina® TruSeq® Nano DNA Library Prep kits.

  • 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.

Protocol 1: TruSeq Nano DNA v1.0

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Fragment DNA (TruSeq Nano DNA v1.0)

  • Master Step Name = Fragment DNA v1.0

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • TruSeq Nano DNA LT Library Prep Kit - Set A, Set B

      • Supplier = Illumina

      • Catalog Number = Set A: FC-121-4001, Set B: FC-121-4002

Automations

Normalize gDNA (Nano)

  • 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:http} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'if ( step.::Target Insert Size (bp):: == 350 ) { output.::Sample Volume (ul):: = 100 / output.::Concentration:: } ; if ( step.::Target Insert Size (bp):: == 550 ) { output.::Sample Volume (ul):: = 200 / output.::Concentration:: } ; output.::RSB Volume (ul):: = 52.5 - output.::Sample Volume (ul):: ; output.::Target Insert Size (bp):: = step.::Target Insert Size (bp)::' -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}"
Normalize gDNA (PCR Free)

  • 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 true -h false -exp 'if ( step.::Target Insert Size (bp):: == 350 ) { output.::Sample Volume (ul):: = 1000 / output.::Concentration:: } ; if ( step.::Target Insert Size (bp):: == 550 ) { output.::Sample Volume (ul):: = 2000 / output.::Concentration:: } ; output.::RSB Volume (ul):: = 55 - output.::Sample Volume (ul):: ; output.::Target Insert Size (bp):: = step.::Target Insert Size (bp)::' -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

    Cycles/Burst

    Numeric Dropdown

    • Custom Entries

    • Presets

      • 200

    Duration (seconds)

    Numeric Dropdown

    • Custom Entries

    • Presets

      • 65

      • 50

      • 45

      • 25

    • Decimal Places Displayed = 0

    Duty Factor (%)

    Numeric Dropdown

    • Custom Entries

    • Presets

      • 20

      • 5

      • 10

    • Decimal Places Displayed = 0

    Intensity

    Numeric Dropdown

    • Custom Entries

    • Presets

      • 5

      • 2

    • Decimal Places Displayed = 1

    Mode

    Text Dropdown

    • Custom Entries

    • Presets

      • Frequency sweeping

      • -

    Peak/Displayed Power (W)

    Numeric Dropdown

    • Custom Entries

    • Presets

      • 50

      • 175

      • 23

      • 14

      • 9

      • 7

    • Decimal Places Displayed = 0

    Target Insert Size (bp)

    Numeric Dropdown

    • Required Field

    • Custom Entries

    • Presets

      • 350

      • 550

    • Decimal Places Displayed = 0

    Temperature (oC)

    Numeric Dropdown

    • Custom Entries

    • Presets

      • 20

      • 6

  • 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

      Derived Sample

      Concentration

      Numeric

      Required Field

      Decimal Places Displayed = 2

      Derived Sample

      Conc. Units

      Text

      Required Field

      Derived Sample

      RSB Volume (ul)

      Numeric

      Read Only

      Decimal Places Displayed = 2

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Sample Volume (ul)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Target Insert Size (bp)

      Numeric Dropdown

      Custom Entries

      Presets

      • 350

      • 550

      Project

      Project Name

      Built-in

Step 2: Repair Ends and Select Library Size (TruSeq Nano DNA v1.0)

  • Master Step Name = Repair Ends v1.0

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {SubmittedSampleName}

  • Reagent Kits

    • TruSeq Nano DNA LT Library Prep Kit - Set A, Set B

      • Supplier = Illumina

      • Catalog Number = Set A: FC-121-4001, Set B: FC-121-4002

Automations

SPB Dilution

  • 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 false -h false -exp 'step.::Total Number of Samples:: = step.::Total Number of 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 'if(input.::Target Insert Size (bp):: == 350) { step.::SPB (ml):: = (step.::Total Number of Samples:: * 109.25) / 1000} ; if(input.::Target Insert Size (bp):: == 350) { step.::PCR Grade Water (ml):: = (step.::Total Number of Samples:: * 74.75) / 1000 } ; if(input.::Target Insert Size (bp):: == 550) { step.::SPB (ml):: = (step.::Total Number of Samples:: * 92) / 1000} ; if(input.::Target Insert Size (bp):: == 550) { step.::PCR Grade Water (ml):: = (step.::Total Number of Samples:: * 92) / 1000 } ; output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -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

      Target Insert Size (bp)

      Numeric Dropdown

      Custom Entries

      • Presets

        • 350

        • 550

      • Decimal Places Displayed = 0

      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

    PCR Grade Water (ml)

    Numeric

    Decimal Places Displayed = 2

    SPB (ml)

    Numeric

    Decimal Places Displayed = 2

    Thermal Cycler Program

    Text

    Default = ERP

  • Step File Placeholders

    • Next Step Log - 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

      Well

      Built-in

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Target Insert Size (bp)

      Numeric Dropdown

      Custom Entries

      Presets

      • 350

      • 550

      Project

      Project Name

      Built-in

Step 3: Adenylate 3' Ends (TruSeq Nano DNA v1.0)

  • Master Step Name = Adenylate 3' Ends v2.0

  • Step Type = No Outputs

  • Reagent Kits

    • TruSeq Nano DNA LT Library Prep Kit - Set A, Set B

      • Supplier = Illumina

      • Catalog Number = Set A: FC-121-4001, Set B: FC-121-4002

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 = Column

  • 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

      Target Insert Size (bp)

      Numeric Dropdown

      Custom Entries

      • Presets

        • 350

        • 550

      • Decimal Places Displayed = 0

      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

    Thermal Cycler Program

    Text

    Default = ATAIL70

  • Step File Placeholders

    • Log File - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Column

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Target Insert Size (bp)

      Numeric Dropdown

      Custom Entries

      Presets

      • 350

      • 550

      Project

      Project Name

      Built-in

Step 4: Ligate Adapters (TruSeq Nano DNA v1.0)

  • Master Step Name = Ligate Adapters v2.0

  • Step Type = Add Labels

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {SubmittedSampleName}

  • Reagent Kits

    • TruSeq Nano DNA LT Library Prep Kit - Set A, Set B

      • Supplier = Illumina

      • Catalog Number = Set A: FC-121-4001, Set B: FC-121-4002

Automations

Copy to Output

  • 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/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -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}"
Set Next Step & Copy to Input

  • 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 'nextStep = ::ADVANCE:: ; output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::'  -log {compoundOutputFileLuid0}"

Queue/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

      Container

      Container Name

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Target Insert Size (bp)

      Numeric Dropdown

      Custom Entries

      • Presets

        • 350

        • 550

      • Decimal Places Displayed = 0

      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

Add Labels

  • Label Groups

    • TruSeq DNA HT

    • TruSeq DNA LT

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Comment

    Multiline Text

    Thermal Cycler Program

    Text

    Default = ATAIL70

    80% EtOH Prep Date

    Date

  • Step File Placeholders

    • Log File - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Column

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Reagent Name

      Built-in

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Target Insert Size (bp)

      Numeric Dropdown

      Custom Entries

      Presets

      • 350

      • 550

      Project

      Project Name

      Built-in

Step 5: PCR Amplification (TruSeq Nano DNA v1.0)

  • Master Step Name = PCR Amplification (TruSeq Nano DNA v1.0.10)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {SubmittedSampleName}

  • Reagent Kits

    • TruSeq Nano DNA LT Library Prep Kit - Set A, Set B

      • Supplier = Illumina

      • Catalog Number = Set A: FC-121-4001, Set B: FC-121-4002

The version of PCR Amplification master step name may be different depending on the version of IPP installed.

Automations

Copy to Output

  • 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/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -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 = Column

  • 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

      Target Insert Size (bp)

      Numeric Dropdown

      Custom Entries

      • Presets

        • 350

        • 550

      • Decimal Places Displayed = 0

      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

    Thermal Cycler Program

    Text

    Default = PCRNano

    80% EtOH Prep Date

    Date

  • Step File Placeholders

    • Log File - Automatically attached

  • Sample Table

    • Sample Display Default = Collapse

    • Well Sort Order = Column

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Target Insert Size (bp)

      Numeric Dropdown

      Custom Entries

      Presets

      • 350

      • 550

      Project

      Project Name

      Built-in

Step 6: Validate Libraries (TruSeq Nano DNA v1.0)

  • Master Step Name = Validate Libraries (TruSeq Nano DNA v1.0.10)

  • Step Type = Standard QC

  • Measurement Generation = Fixed, 4

  • Naming Convention = {SubmittedSampleName}_{OutputItemSubsetNumber} of {OutputItemSubsetTotal}

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

Automations

Set Dilution Factor

  • 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/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'if (output.name.contains(::_1 of 4::)) {output.::Dilution Factor:: = ::1:10000::} ; if (output.name.contains(::_2 of 4::)) {output.::Dilution Factor:: = ::1:10000::} ; if (output.name.contains(::_3 of 4::)) {output.::Dilution Factor:: = ::1:20000::} ; if (output.name.contains(::_4 of 4::)) {output.::Dilution Factor:: = ::1:20000::}' -log {compoundOutputFileLuid0}"
Calculate Molarity and Assign 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 {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp ' if (output.::Dilution Factor:: == ::1:10000:: && input.::Target Insert Size (bp):: == 350) {output.::Molarity (nM):: = ((output.::Concentration (pM):: * 10000) * (452 / 470)) / 1000} ; if (output.::Dilution Factor:: == ::1:20000:: && input.::Target Insert Size (bp):: == 350) {output.::Molarity (nM):: = ((output.::Concentration (pM):: * 20000) * (452 / 470)) / 1000} ; if (output.::Dilution Factor:: == ::1:10000:: && input.::Target Insert Size (bp):: == 550) {output.::Molarity (nM):: = ((output.::Concentration (pM):: * 10000) * (452 / 670)) / 1000} ; if (output.::Dilution Factor:: == ::1:20000:: && input.::Target Insert Size (bp):: == 550) {output.::Molarity (nM):: = ((output.::Concentration (pM):: * 10000) * (452 / 670)) / 1000}' -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:computeReplicateAverage -src 'Molarity (nM)' -dest 'Molarity (nM)' -exclude 'Exclude' -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 true -h false -exp 'if (output.::Molarity (nM):: >= 10 && output.::Molarity (nM):: <= 250) { output.QC = true } else { output.QC = false } ; if (input.::Molarity (nM):: >= 10 && input.::Molarity (nM):: <= 250) { input.QC = true } else { input.QC = false }' -log {compoundOutputFileLuid0}"
Set Next Steps - 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 (input.QC == true) { nextStep = ::ADVANCE:: } else { nextStep = ::ESCALATE:: }' -log {compoundOutputFileLuid0}"

Queue/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

      Container

      Container Name

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Target Insert Size (bp)

      Numeric Dropdown

      Custom Entries

      • Presets

        • 350

        • 550

      • Decimal Places Displayed = 0

      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

  • Step File Placeholders

    • Log File - Manually uploaded

  • Sample Table

    • Enable QC Flags = Yes

    • Sample Display Default = Expand

    • Well Sort Order = Column

    • File Column Options

      • File Column Display = Hide

      • File Attachment Method = Manual

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Molarity (nM)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Sample Name

      Built-in

      Measurement

      Concentration (pM)

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Dilution Factor

      Text

      Read Only

      Measurement

      Exclude

      Toggle Switch

      Default = None Set

      Measurement

      Molarity (nM)

      Numeric

      Decimal Places Displayed = 2

      Project

      Project Name

      Built-in

Step 7: Normalize Libraries (TruSeq Nano DNA v1.0)

  • Master Step Name = Normalize Libraries 2 v2.0.10

  • Step Type = Standard

  • Measurement Generation = Fixed, 1

  • Naming Convention = {InputItemName}

The version of Normalize Libraries 2 master step name may be different depending on the version of IPP installed.

Automations

Normalization Calculations - Option 2

  • 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:http} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'output.::Molarity (nM):: = input.::Molarity (nM):: ; if (output.::Molarity (nM):: <= step.::Target Normalization (nM)::) {output.::Sample Volume (ul):: = step.::Sample Volume (ul):: ; output.::Buffer Volume (ul):: = 0 ; output.::Normalized Molarity (nM):: = output.::Molarity (nM)::} else {output.::Sample Volume (ul):: = step.::Sample Volume (ul):: ; output.::Buffer Volume (ul):: = ((output.::Molarity (nM):: * step.::Sample Volume (ul)::) / step.::Target Normalization (nM)::) - step.::Sample Volume (ul):: ; output.::Normalized Molarity (nM):: = step.::Target Normalization (nM)::}' -log {compoundOutputFileLuid0}"
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}"
Set Next Steps - 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 (input.QC == true) { nextStep = ::ADVANCE:: } else { nextStep = ::ESCALATE:: }' -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 value and actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.

Queue/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

      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

    Sample Volume (ul)

    Numeric

    Required Field

    • Default = 10

    • Decimal Places Displayed = 0

    Target Normalization (nM)

    Numeric

    Required Field

    • Default = 10

    • Decimal Places Displayed = 0

  • Step File Placeholders

    • Log File - Automatically attached

  • Sample Table

    • Sample Display Default = Expand

    • Well Sort Order = Column

    • Table Columns - Global Fields

      Category

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Buffer Volume (ul)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Molarity (nM)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Normalized Molarity (nM)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Sample Volume (ul)

      Numeric

      Decimal Places Displayed = 2

      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

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