Nextera Mate Pair v1.0

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Protocol 1: Nextera Mate Pair v1.0

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Tagment Genomic DNA (Nextera Mate Pair v1.0)

Master Step Name = Tagment Genomic DNA (Nextera Mate Pair v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- Nextera Mate Pair Library Prep Kit - Box 1
  - Supplier = Illumina
  - Catalog Number = FC-132-1001
- Nextera Mate Pair Library Prep Kit - Box 2
  - Supplier = Illumina
  - Catalog Number = FC-132-1001
- Zymo Genomic DNA Clean & Concentrator
  - Supplier = Zymo Research
  - Catalog Number = D4010 (25 preps) or D4011 (100 preps)

Automations

Master Mix 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 'if (output.::Gel Type:: == ::Gel-Free::) {output.::Sample Volume (ul):: = 1000 / input.::Concentration (ng/ul):: ; output.::Water Per Sample (ul):: = 76 - output.::Sample Volume (ul)::} ; if (output.::Gel Type:: == ::Gel-Plus::) {output.::Sample Volume (ul):: = 4000 / input.::Concentration (ng/ul):: ; output.::Water Per Sample (ul):: = 308 - output.::Sample Volume (ul)::}' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
- Expanded View Fields

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 2: Bioanalyzer QC (DNA) (Nextera Mate Pair v1.0)

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

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 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' 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}"

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 = Row
Sample Table
- Column Headers
- Expanded View Fields

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Row
Destination Containers
- BioAnalyzer DNA 7500 and DNA 1200 Chip
- BioAnalyzer DNA High Sensitivity Chip

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Bioanalyzer Input File - Automatically attached
- Bioanalyzer Input File Generation Log - 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 = Row
- File Column Options
  - File Column Display = Hide
  - File Attachment Method = Auto
- Table Columns - Global Fields

Step 3: Strand Displacement (Nextera Mate Pair v1.0)

Master Step Name = Strand Displacement (Nextera Mate Pair v1.0.10)
Step Type = No Outputs
Reagent Kits
- Nextera Mate Pair Library Prep Kit - Box 1
  - Supplier = Illumina
  - Catalog Number = FC-132-1001
- Nextera Mate Pair Library Prep Kit - Box 2
  - Supplier = Illumina
  - Catalog Number = FC-132-1001

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
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields

Step 4: Purify the DNA (Nextera Mate Pair v1.0)

Master Step Name = Purify the DNA (Nextera Mate Pair v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- AMPure XP Beads
  - Supplier = Beckman Coulter Genomics
  - Catalog Number = A63881
  - Website = https://www.beckmancoulter.com/wsrportal/wsr/research-and-discovery/products-and-services/nucleic-acid-sample-preparation/agencourt-ampure-xp-pcr-purification/index.htm
- Nextera Mate Pair Library Prep Kit - Box 2
  - Supplier = Illumina
  - Catalog Number = FC-132-1001

Automations

Set Next Step based on Gel Type

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.::Gel Type:: = input.::Gel Type:: ; if (step.::Next Step:: == ::Gel-Free::) {nextStep = ::Bioanalyzer QC (DNA) (Nextera Mate Pair v1.0.10)::} ; if (step.::Next Step:: == ::Gel-Plus Pippin Prep::) {nextStep = ::Pippin Prep Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0.10)::} ; if (step.::Next Step:: == ::Gel-Plus Agarose Gel::) {nextStep = ::Agarose Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0.10)::}' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields

Step 5: Pippin Prep Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0)

Master Step Name = Pippin Prep Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- Pippin Prep 0.75% agarose cassette and solutions
  - Catalog Number = CSD7510
- Zymo Genomic DNA Clean & Concentrator
  - Supplier = Zymo Research
  - Catalog Number = D4010 (25 preps) or D4011 (100 preps)

Automations

Set Next Step & Copy Gel Type

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:: ; output.::Gel Type:: = input.::Gel Type::' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
- Gel Image - Manually uploaded
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 6: Agarose Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0)

Master Step Name = Agarose Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- 1 kb plus DNA ladder
  - Supplier = Invitrogen
  - Catalog Number = 10787-018
- 6X gel loading dye
  - Supplier = BioLabs
  - Catalog Number = B7021S
- 50X TAE buffer
  - Supplier = Bio-Rad
  - Catalog Number = 161-0743
- DNA Gel Extraction kit - Zymoclean Large Fragment DNA Recovery Kit
  - Supplier = Zymo Research
  - Catalog Number = D4045
- Megabase Agarose
  - Supplier = Bio-Rad
  - Catalog Number = 161-3108
- Nextera Mate Pair Library Prep Kit – Box 2
  - Supplier = Illumina
  - Catalog Number = FC-132-1001
- SYBR Safe
  - Supplier = Invitrogen
  - Catalog Number = S33102

Automations

Set Next Step - Advance

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 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Set Next Step & Copy Gel Type

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:: ; output.::Gel Type:: = input.::Gel Type::' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
- Gel Image - Manually uploaded
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields

Step 7: Bioanalyzer QC (DNA) (Nextera Mate Pair v1.0)

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

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 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' script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"

Set Next Step & Copy to Input

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

Set Next Step - Output PASS/FAIL

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
- Expanded View Fields

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Row
Destination Containers
- BioAnalyzer DNA 7500 and DNA 1200 Chip
- BioAnalyzer DNA High Sensitivity Chip

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Bioanalyzer Input File - Automatically attached
- Bioanalyzer Input File Generation Log - 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 = Row
- File Column Options
  - File Column Display = Hide
  - File Attachment Method = Auto
- Table Columns - Global Fields

Step 8: Circularize DNA (Nextera Mate Pair v1.0)

Master Step Name = Circularize DNA (Nextera Mate Pair v1.0.10)
Step Type = No Outputs
Reagent Kits
- Nextera Mate Pair Library Prep Kit - Box 1
  - Supplier = Illumina
  - Catalog Number = FC-132-1001

Automations

Master Mix Calculations