TruSeq DNA Exome v2.0

Overview

The TruSeq DNA Exome v2.0 includes the following functionality:

• Preconfigured TruSeq DNA Exome v2.0 protocol that supports the preparation of 96 indexed, paired-end libraries, followed by enrichment using reagents provided in an Illumina® TruSeq® Exome Kit.

• 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 to any Illumina sequencing instrument.

Protocol 1: Library Prep (TruSeq DNA Exome v2.0)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Normalize DNA (TruSeq DNA Exome v2.0)

• Master Step Name = Normalize DNA (TruSeq DNA Exome v2.0.10)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • TruSeq Exome Kit

    • Supplier = Illumina

    • Catalog Number = 24 - 20020614; 96 - 20020615

    • Website = www.illumina.com

Automations

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.::Concentration:: = input.::Concentration:: ; \
output.::Conc. Units:: = input.::Conc. Units:: ; \
output.::Sample Volume (uL):: = step.::DNA Amount (ng):: / output.::Concentration:: ; \
output.::Shearing Buffer Mix (uL):: = step.::Total Volume (uL):: - output.::Sample Volume (uL)::' \
-log {compoundOutputFileLuid0}"

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Column

• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)
• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 2: Fragment DNA (TruSeq DNA Exome v2.0)

• Master Step Name = Fragment DNA (TruSeq Exome v1.0)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {SubmittedSampleName}

• Reagent Kits

  • TruSeq Exome Kit

    • Supplier = Illumina

    • Catalog Number = 24 - 20020614; 96 - 20020615

    • Website = www.illumina.com

Automations

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'output.::Sample Volume (ul):: = 100 / input.::Concentration (ng/ul):: ; output.::Buffer Volume (ul):: = 50 - output.::Sample Volume (ul):: ' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Column

• Destination Containers

  • Tube

  • 96 well plate

Record Details

• Step Data (Master Step Fields)
• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 3: Clean Up Fragmented DNA (TruSeq DNA Exome v2.0)

• Master Step Name = TruSeq DNA Exome v2.0.10

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • TruSeq Exome Kit

    • Supplier = Illumina

    • Catalog Number = 24 - 20020614; 96 - 20020615

    • Website = www.illumina.com

Automations

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)

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Column

• Destination Containers

  • Tube

  • 96 well plate

Record Details

• Step Data (Master Step Fields)
• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 4: Repair Ends and Select Library Size (TruSeq DNA Exome v2.0)

• Master Step Name = TruSeq DNA Exome v2.0.10

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • TruSeq Exome Kit

    • Supplier = Illumina

    • Catalog Number = 24 - 20020614; 96 - 20020615

    • Website = www.illumina.com

Automations

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)

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Column

• Destination Containers

  • Tube

  • 96 well plate

Record Details

• Step Data (Master Step Fields)
• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 5: Ligate Adapters (TruSeq DNA Exome v2.0)

• Master Step Name = Ligate Adapters (TruSeq DNA Exome v2.0.10)

• Step Type = Add Labels

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}-{AppliedReagentLabels}

• Reagent Kits

  • TruSeq Exome Kit

    • Supplier = Illumina

    • Catalog Number = 24 - 20020614; 96 - 20020615

    • Website = www.illumina.com

Automations

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)

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Column

• Destination Containers

  • Tube

  • 96 well plate

Add Labels

• Label Groups

  • IDT-ILMN TruSeq DNA-RNA UD 24 Indexes

  • IDT-ILMN TruSeq DNA-RNA UD 24 Indexes Plate

  • IDT-ILMN TruSeq DNA-RNA UD 96 Indexes Plate

  • TruSeq Exome

  • TruSeq Exome HT

  • TruSeq Exome LT

Record Details

• Step Data (Master Step Fields)
• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 6: Enrich DNA Fragments (TruSeq DNA Exome v2.0)

• Master Step Name = TruSeq DNA Exome v2.0.10

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • TruSeq Exome Kit

    • Supplier = Illumina

    • Catalog Number = 24 - 20020614; 96 - 20020615

    • Website = www.illumina.com

Automations

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)

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Column

• Destination Containers

  • Tube

  • 96 well plate

Record Details

• Step Data (Master Step Fields)
• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • Table Columns - Global Fields

Step 7: Qubit DNA QC (TruSeq DNA Exome v2.0)

• Master Step Name = Qubit DNA QC (TruSeq Exome v1.0)

• Step Type = Standard QC

• Measurement Generation = Fixed, 2

• Naming Convention = {SubmittedSampleName}

Automations

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:computeReplicateAverage -src 'Concentration' -dest 'Concentration' -log {compoundOutputFileLuid3} && /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}  && /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 'input.::Concentration:: = output.::Concentration::' -log {compoundOutputFileLuid3}"

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)

Record Details

• Step Data (Master Step Fields)
• Step File Placeholders

  • Qubit Result File - Manually uploaded

  • QC Assignment Log File - Manually uploaded

  • QC Assignment Report File - Manually uploaded

  • Log File - 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

Step 8: Bioanalyzer QC (TruSeq DNA Exome v2.0)