Illumina Preset Protocol - Illumina DNA Prep with Enrichment (S) Tagmentation

Protocol 1: Prep Sample (Illumina DNA Prep with Enrichment (S) Tagmentation)

Master Step 1: Sort Sample (Illumina DNA Prep with Enrichment (S) Tagmentation)

Master Step Type: No Outputs

Input = Blood, Saliva, gDNA, FFPE DNA

Output = Blood Lysis, Saliva Lysis, gDNA, FFPE DNA

Record Details

Section

Subsection

Setting

Value

Specification

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Sample Type

Text Dropdown

Global field - derived sample

Presets

• Blood
• Saliva
• gDNA
• FFPE DNA
Automation

Automation Name

Setting

Value

Specification

Sort & Set Next Step

Trigger Location

Record Details

 

 

Trigger Style

Automatic upon exit

 

 

 

 

Command line

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 (input.::NFE Sample Type:: == ::Blood:: ) {nextStep=::Blood Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.0):: } ; if (input.::NFE Sample Type:: == ::Saliva:: ) {nextStep=::Saliva Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.0):: } ; if (input.::NFE Sample Type:: == ::gDNA:: ) {nextStep=::Qubit gDNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.0):: } ; if (input.::NFE Sample Type:: == ::FFPE DNA::) {nextStep=::Qubit FFPE DNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.0):: }' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Automatic

Safe Stopping Point

 

Master Step 2: Blood Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation)

Step type: Standard

Input = Blood

Output = Blood Lysis

This protocol is expected to generate > 100 ng of DNA output at the end of the blood lysis step.

Reagent Kits

Kit Name

Supplier

Cat. #

Flex Lysis Reagent Kit

Illumina

20015884

Agencourt AMPure XP beads, 5 ml

Beckman Coulter

A63880
Placement

Setting

Value

Specification

Destination Containers

96 well plate

 

Placement Pattern

Column

 

Placement Screen

Manual

 
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Thermal Cycler Program

Text

Default - BLP
   

Total Samples

Numeric

Calculated = Total Samples + 1

 

 

BLB (μl)

Numeric

Calculated = Total Samples * 7 * 1.1

 

  

PK1 (μl)

Numeric

Calculated = Total Samples * 2 * 1.1
   

Water (μl)

Numeric

Calculated = Total Samples * 31 * 1.1
   

80% EtOH Prep Date

Date

  

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

NFE Sample

Text
• Global field - derived sample
• Copied from previous step
Automation

Automation Name

Setting

Value

Specification

Calculate Total Samples & Master Mix

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon entry

  
     

Command line

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 Samples:: = step.::Total 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 'output.::NFE Sample Type:: = input.::NFE Sample Type:: ; \

step.::BLB (uL):: = step.::Total Samples:: * 1.1 * 7 ; \

step.::PK1 (uL):: = step.::Total Samples:: * 1.1 * 2 ; \

step.::Water (uL):: = step.::Total Samples:: * 1.1 * 31' \

-log {compoundOutputFileLuid0}"

Set Next Step - Remove & Copy NFE Sample Type

Trigger Location

Record Details

 

 

Trigger Style

Automatic upon exit

 

 

 

 

Command line

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:: ; \

output.::NFE Sample Type:: = input.::NFE Sample Type::' \

-log {compoundOutputFileLuid0}"

Route NFE - Blood

Trigger Location

Step

  
 

Trigger Style

Automatic upon exit

  
     

Command line

bash -l -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 'NFE Sample Type' \

--FIELD_VALUE 'Blood' \

--WORKFLOW 'Illumina DNA Prep with Enrichment (S) Tagmentation v1.0' \

--STEP 'Tagment Genomic DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' "

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Automatic

Safe Stopping Point

 

Master Step 3: Saliva Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation)

Master Step Type: Standard

Input = Saliva

Output = Saliva Lysis

Reagent Kits

Kit Name

Supplier

Cat. #

Agencourt AMPure XP beads, 5 ml

Beckman Coulter

A63880
Placement

Setting

Value

Specification

Destination Containers

96 well plate

  

Placement Pattern

Column

 

Placement Screen

Manual

 
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

80% EtOH Prep Date

Date

  

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

NFE Sample

Text
• Global field - derived sample
• Copy from previous step
   

Sample Volume (μl)

Numeric

  
   

80% EtOH (μl)

Numeric

  
   

Water for Resuspension (μl)

Numeric

Default - 30
Automation

Automation Name

Setting

Value

Specification

Copy NFE Sample Type and Set UDFs

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon entry

  
     

Command line

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.::NFE Sample Type:: = input.::NFE Sample Type:: ; \

output.::Sample Volume (uL):: = 30 ; \

output.::80% EtOH (uL):: = 150 ; \

output.::Water for Resuspension (uL):: = 30' \

-log {compoundOutputFileLuid0}"

Set Next Step - Remove

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon exit

  
     

Command line

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}"

Route NFE - Saliva

Trigger Location

Step

 

 

Trigger Style

Automatic upon exit

 

 

 

 

Command line

bash -l -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 'NFE Sample Type' \

--FIELD_VALUE 'Saliva' \

--WORKFLOW 'Illumina DNA Prep with Enrichment (S) Tagmentation v1.0' \

--STEP 'Tagment Genomic DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' "

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Automatic

Safe Stopping Point

 

Master Step 4: Qubit gDNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation)

Master Step Type: Standard QC

Input = gDNA (10–1000 ng)

Output = Measurement

Placement

Setting

Value

Specification

Placement Pattern

Tube

  

Placement Screen

Auto

 
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Criteria 1 - Source Data Field

  

Concentration
   

Criteria 1 - Operator

  

>=
   

Criteria 1 - Threshold Value

    
   

Criteria 2 - Source Data Field

  

Concentration
   

Criteria 2 - Operator

  

<=
   

Criteria 2 - Threshold Value

    

Step File Placeholders

 

File Name

Log

Auto
     

QC Log File

Auto
     

QC Result File

Auto
     

Upload File

Manual

Sample Table

Table Columns

Concentration

Numeric

Derived Sample and Measurement custom field
   

Conc. Units

Text

  
   

NFE Sample

Text

Copied from previous step
Automation

Automation Name

Setting

Value

Specification

Assign QC Flags

    

Command line

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 and Copy Concentration

    

Command line

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

Next Step

Setting

Value

Start Next Step

Automatic

Assign Next Step

Automatic

Must move forward

 

Master Step 5: Dilute gDNA (Illumina DNA Prep with Enrichment (S) Tagmentation)

Master Step Type: Standard

Input = gDNA with concentration

Output = Diluted DNA (10-1000 ng)

Placement

Setting

Value

Specification

Destination Containers

96 well plate

  

Placement Pattern

Column

 

Placement Screen

Manual

 
Reagent Kits

Kit Name

Supplier

Cat. #

Illumina DNA Prep -Tagmentation (S) Beads

Illumina

20025519; 20025520
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Desired gDNA Input (ng)

Numeric

Default - 10-1000
   

Dilution Buffer

Text Dropdown

• 10 mM Tris-HCI, pH 7.5–8.5
• RSB
   

Notes

Multiline Text

Preset = For human gDNA samples and other large complex genomes, the recommended minimum gDNA input is 50 ng.
   

Sample Volume (μl)

Numeric

Default - 5

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Concentration

Numeric

Copy from previous step
   

Conc. Units (ng/μl)

Text

  
   

Total Volume (μl)

Numeric

Calculated = (Concentration * Sample Volume (μl)) / Desired gDNA Input (ng)
   

Dilution Volume (μl)

Numeric

Calculated = Total Volume (μl) - Sample Volume (μl)
   

Desired gDNA Input (ng)

Numeric

Copied from step field
Automation

Automation Name

Setting

Value

Specification

Copy Concentration

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon entry

  
     

Command line

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.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units::' \

-log {compoundOutputFileLuid0}"

Calculate Dilution Volume & Total Volume

Trigger Location

Record Details

  
 

Trigger Style

Manual

  
     

Command line

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.::Total Volume (uL):: = (output.::Concentration:: * step.::Sample Volume (uL)::) / step.::Desired gDNA Input (ng):: ; \

output.::Dilution Volume (uL):: = output.::Total Volume (uL):: - step.::Sample Volume (uL)::' \

-log {compoundOutputFileLuid0}"

Set Next Step - Remove & Copy NFE Sample Type and Desired gDNA Input (ng)

Trigger Location

Record Details

  

 

Trigger Style

Automatic upon exit

 
     

Command line

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:: ; \

output.::NFE Sample Type:: = input.::NFE Sample Type:: ; \

output.::Desired gDNA Input (ng):: = step.::Desired gDNA Input (ng)::' \

-log {compoundOutputFileLuid0}"

Route NFE - gDNA

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon entry

  
     

Command line

bash -l -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 'NFE Sample Type' \

--FIELD_VALUE 'gDNA' \

--WORKFLOW 'Illumina DNA Prep with Enrichment (S) Tagmentation v1.0' \

--STEP 'Tagment Genomic DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' "

Next Step

Setting

Value

Start Next Step

Automatic

Assign Next Step

Automatic

Must move forward

 

Master Step 6: Qubit FFPE DNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation)

Step Type: Standard QC

Input = FFPE DNA (50–1000 ng)

Output = Measurement

Standard QC

Placement

Setting

Value

Destination Containers

Tube
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Criteria 1 - Source Data Field

  

Concentration
   

Criteria 1 - Operator

  

>=
   

Criteria 1 - Threshold Value

    
   

Criteria 2 - Source Data Field

  

Concentration
   

Criteria 2 - Operator

  

<=
   

Criteria 2 - Threshold Value

    

Step File Placeholders

 

File Name

Log

Auto
     

QC Log File

Auto
     

QC Result File

Auto
     

Upload File

Manual

Sample Table

Table Columns

Concentration

Numeric

Global fields - Derived Sample and Measurement
   

Conc. Units

Text

Global fields - Derived Sample and Measurement
   

NFE Sample type

Text

Copied from previous step
Automation

Automation Name

Setting

Value

Specification

Assign QC Flags

    

Command line

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 and Copy Concentration

    

Command line

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

Next Step

Setting

Value

Start Next Step

Automatic

Assign Next Step

Automatic

Must move forward

 

Master Step 7: Dilute FFPE DNA (Illumina DNA Prep with Enrichment (S) Tagmentation)

Input = FFPE DNA

Output = Diluted DNA (50-1000 ng)

Reagent Kits

Kit Name

Supplier

Cat. #

Illumina DNA Prep -Tagmentation (S) Beads

Illumina

20025519; 20025520
Placement

Setting

Value

Destination Containers

96 well plate
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Desired gDNA Input (ng)

  

50-1000
   

Dilution Buffer

Text Dropdown
• 10 mM Tris-HCI, pH 7.5–8.5
• RSB
   

Sample Volume (μl)

Numeric

Default - 5

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Concentration

Numeric

Copied from previous step
   

Conc. Units (ng/μl)

Text

  
   

Total Volume (μl)

Numeric

Calculated = (Concentration * Sample Volume (μl)) / (Desired gDNA Input (ng) * 5)
   

Dilution Volume (μl)

Numeric

Calculated = Total Volume (μl) - Sample Volume (μl)
   

Desired gDNA Input (ng)

Numeric

Copied from step field
Automation

Automation Name

Setting

Value

Specification

Copy Concentration

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon entry

  
     

Command line

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.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units::' \

-log {compoundOutputFileLuid0}"

Calculate Dilution Volume & Total Volume

Trigger Location

Record Details

  
 

Trigger Style

Manual

  
     

Command line

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.::Total Volume (uL):: = (output.::Concentration:: * step.::Sample Volume (uL)::) / step.::Desired gDNA Input (ng):: ; \

output.::Dilution Volume (uL):: = output.::Total Volume (uL):: - step.::Sample Volume (uL)::' \

-log {compoundOutputFileLuid0}"

Set Next Step - Advance & Copy NFE Sample Type and Desired gDNA Input

Trigger Location

Record Details

 

 

Trigger Style

Automatic upon exit

 

 

 

 

Command line

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.::NFE Sample Type:: = input.::NFE Sample Type:: ; \

output.::Desired gDNA Input (ng):: = step.::Desired gDNA Input (ng)::' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step

Automatic

Assign Next Step

Automatic

Must move forward

 

Protocol 2: Library Prep (Illumina DNA Prep with Enrichment (S) Tagmentation)

Master Step 1: Tagment Genomic DNA (Illumina DNA Prep with Enrichment (S) Tagmentation)

Input = DNA, Blood Lysis, Saliva Lysis

Output = Tagmented DNA

Reagent Kits

Kit Name

Supplier

Cat. #

Illumina DNA Prep - Tagmentation (S) Beads

Illumina

20025519; 20025520

Illumina DNA/RNA Prep - Tagmentation PCR Reagents

Illumina

20025519; 20025520
Placement

Setting

Value

Destination Containers

96 well plate
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Thermal Cycler Program

  

Default - TAG
   

Total Samples

  
• Default - 0
• Calculated = Total Samples + 1
   

eBLT (μl)

Numeric

Calculated = Total Samples * 11.5 * 1.1
   

TB1 (μl)

Numeric

Calculated = Total Samples * 11.5 * 1.1
   

Desired Input Amount (ng)

Numeric

Range = 50 - 1000 ng
   

Total Volume (μl)

Numeric

Default - 30
   

Thermal Cycler Instructions

Multiline Text

Default

• Choose the preheat lid option and set to 100°C.
• Set the reaction volume to 50 μl.
• 55C for 5minutes.
• Hold at 10C.
   

Notes

Multiline Text

Desired Input Amount should be between 50-1000 ng

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Concentration

Numeric

Global field - derived sample

Copied from previous step
   

Conc. Units (ng/μl)

Text

  
   

Sample Volume (μl)

Numeric

Calculated = Concentration / Desired Input Amount (ng)
   

Nuclease-free water (μl)

Numeric

Calculated = Total Volume (μl) - Sample Volume (μl)
   

NFE Sample Type

Text

Copied from previous step
   

Desired Input Amount (ng)

Numeric

Copied from step field
Automation

Automation Name

Setting

Value

Specification

Calculate Total Samples and Master Mix & Copy Conc. & NFE Sample Type

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon entry

  
     

Command line

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 Samples:: = step.::Total 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 'output.::NFE Sample Type:: = input.::NFE Sample Type:: ; \

step.::eBLT (uL):: = step.::Total Samples:: * 1.1 * 11.5 ; \

step.::TB1 (uL):: = step.::Total Samples:: * 1.1 * 11.5 ; \

if (output.::NFE Sample Type::.contains(::Saliva::) || output.::NFE Sample Type::.contains(::Blood::)) {output.::Concentration:: = 100 ; output.::Conc. Units:: = ::ng/uL::} ; \

if (input.hasValue(::Concentration::)) {output.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units::}' \

-log {compoundOutputFileLuid0}"

Calculate Sample Volume & Water

Trigger Location

Record Details

  
 

Trigger Style

Manual

  
     

Command line

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.::Desired Input Amount (ng):: / output.::Concentration:: ; \

output.::Nuclease-free water (uL):: = step.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \

output.::Desired Input Amount (ng):: = step.::Desired Input Amount (ng):: ; \' \

-log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location

Record Details

 

 

Trigger Style

Automatic upon exit

 

 

 

 

Command line

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}"

Next Step

Setting

Value

Start Next Step

Automatic

Assign Next Step

Automatic

Must move forward

 

Master Step 2: Post Tagmentation Cleanup (Illumina DNA Prep with Enrichment (S) Tagmentation)

Step Type: No Outputs

Input = Tagmented DNA

Output = Cleaned Up Tagmented DNA

Placement

Setting

Value

Specification

Placement Screen

  

None
Reagent Kits

Kit Name

Supplier

Cat. #

Illumina DNA/RNA Prep - Tagmentation Buffers

Illumina

20025519; 20025520
Record Details

Section

Subsection

Setting

Value

Specification

Step File Placeholders

 

File Name

Log

Auto
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Advance

Trigger Location

Record Details

 

 

Trigger Style

Automatic upon exit

 

 

 

 

Command line

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}"

Next Step

Setting

Value

Start Next Step

Automatic

Assign Next Step

Automatic

Must move forward

 

Master Step 3: Amplify Tagmented DNA (Illumina DNA Prep with Enrichment (S) Tagmentation)

Step Type: Add Labels

Input = Cleaned up Tagmented DNA

Output = Amplifed Tagmented DNA

Reagent Kits

Kit Name

Supplier

Cat. #

Illumina DNA Fast Hyb - Enrichment PCR + Buffers

Illumina

20025519; 20025520
Placement

Setting

Value

Specification

Destination Containers

96 well plate

 

Placement Screen

  

None. Uses sample 96 well plate from previous step.
Add Labels

Setting

Value

Label Groups

IDT for Illumina DNA-RNA UD Indexes Set D Tagmentation-label-sheet (1).xlsx
 

IDT for Illumina DNA-RNA UD Indexes Set C Tagmentation-label-sheet (1).xlsx
 

IDT for Illumina DNA-RNA UD Indexes Set B Tagmentation-label-sheet (1).xlsx
 

IDT for Illumina DNA-RNA UD Indexes Set A-D Tagmentation-label-sheet (1).xlsx
 

Location of indexes = UDP Run Setup Resources

Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Thermal Cycler Program

Text

Default - eBLT PCR

 

 

Total Samples

Numeric
• Default - 0
• Calculated = Total Samples + 1

 

  

EPM (μl)

Numeric

Calculated = Total Samples * 23 *1.1
   

Nuclease-free water (μl)

Numeric

Calculated = Total Samples * 23 *1.1
   

Thermal Cycler Instructions

Multiline Text

Default

• Choose the preheat lid option and set to 100°C Set the reaction volume to 50 μl
• 72C for 3 minutes
• 98C for 3 minutes

X cycles of:

• X = 98C for 20 seconds
• X = 0C for 30 seconds
• X = 72C for 1 minute
• 72C for 3 minutes Hold at 10C

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

PCR Cycles

Numeric

Preset with script
Automation

Automation Name

Setting

Value

Specification

Calculate Total Samples, Master Mix, Copy NFE Sample Type and Set PCR Cycles

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon entry

  
     

Command line

/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 Samples:: = step.::Total 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 'output.::NFE Sample Type:: = input.::NFE Sample Type:: ; \

step.::EPM (uL):: = step.::Total Samples:: * 1.1 * 23 ; \

step.::Nuclease-free water (uL):: = step.::Total Samples:: * 1.1 * 23 ; \

if (output.::NFE Sample Type:: == ::Saliva::) {output.::PCR Cycles:: = 9} ; \

if (output.::NFE Sample Type:: == ::Blood::) {output.::PCR Cycles:: = 9} ; \

if (output.::NFE Sample Type:: == ::gDNA::) {if (input.::Desired Input Amount:: >= 10 && input.::Desired Input Amount:: <= 49) {output.::PCR Cycles:: = 12}} ; \

if (output.::NFE Sample Type:: == ::gDNA::) {if (input.::Desired Input Amount:: >= 50 && input.::Desired Input Amount:: <= 1000) {output.::PCR Cycles:: = 9}} ; \

if (output.::NFE Sample Type:: == ::FFPE DNA::) {if (input.::Desired Input Amount:: >= 50 && input.::Desired Input Amount:: <= 1000) {output.::PCR Cycles:: = 12}} ; \\

-log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location

Record Details

 

 

Trigger Style

Automatic upon exit

 

 

 

 

Command line

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}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Automatic

Safe Stopping Point

 

Master Step 4: Clean Up Libraries (Illumina DNA Prep with Enrichment (S) Tagmentation)

Step Type: Standard

Input = Amplifed Tagmented DNA

Output = Cleaned up libraries

Reagent Kits

Kit Name

Supplier

Cat. #

Agencourt AMPure XP purification beads

Beckman Coulter

A63880

Illumina DNA Prep -Tagmentation (S) Beads

Illumina

20025519; 20025520
Placement

Setting

Value

Destination Containers

96 well plate
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

80% EtOH Prep Date

Date

  

Step File Placeholders

 

File Name

Log

Auto
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Advance

Trigger Location

Record Details

 

 

Trigger Style

Automatic upon exit

 

 

 

 

Command line

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}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Automatic

Safe Stopping Point

 

Master Step 5: Bioanalyzer QC Qualify Pre-Enriched Libraries (Illumina DNA Prep with Enrichment (S) Tagmentation)

Step Type: Standard QC

Input = Enriched DNA Fragments

Output = Result File

Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Criteria 1 - Source Data Field

Text

Default: Peak 2 Size - bp
   

Criteria 1 - Operator

Text

Default: >=
   

Criteria 1 - Threshold

Numeric

Default: 300
   

Criteria 2 - Source Data Field

Text

Default: Peak 2 Size - bp
   

Criteria 2 - Operator

Text

Default: <=
   

Criteria 2 - Threshold

Numeric

Default: 400
   

Use strict matching for Bioanalyzer results

Toggle Switch

  

Step File Placeholders

 

File Name

Bioanalyzer Input File

Auto
     

Bioanalyzer Input File Generation Log File

Auto
     

Bioanalyzer XML Result File

• Manual
• Required
     

Result File

• Manual
• Optional
     

PDF Summary File

• Manual
• Optional
     

Bioanalyzer XML Parsing Log File

Auto
     

QC Assignment Log File

Auto
     

QC Assignment Report

Auto
Automation

Automation Name

Setting

Value

Specification

Generate Bioanalyzer Input File

    

Command line

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

    

Command line

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}"

Next Step

Setting

Value

Start Next Step
• Manual

Optional next steps:

• Step 6: Pool Pre-Enriched Libraries by Volume (Illumina DNA Prep with Enrichment (S) Tagmentation)
• Step 7: Qubit (Illumina DNA Prep with Enrichment (S) Tagmentation)

Assign Next Step

 

Safe Stopping Point

 

Master Step 6: Pool Pre-Enriched Libraries (Illumina DNA Prep with Enrichment (S) Tagmentation)

Step Type: Standard

Input = Diluted Pre-Enriched Libraries

Output = Pooled Pre-Enriched Libraries

Reagent Kits

Kit Name

Supplier

Cat. #

Agencourt AMPure XP purification beads

Beckman Coulter

A63880

Illumina DNA Prep -Tagmentation (S) Beads

Illumina

20025519; 20025520
Placement

Setting

Value

Destination Containers

Tube
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Library Pool Plexity

Text Dropdown
• 1-plex
• 12-plex
   

Total Pooled Volume (μl)

Numeric

Read Only

Default = 30

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Pre-Enriched Library Volume (μl)

Numeric
• Global field - derived sample
• Calculated = if Library Pool Plexity = 1-plex then Pre-Enriched Library Volume (μl) = 14 otherwise pre-enriched library volume (μl) = 2.5
   

RSB Volume (μl)

Numeric
• Global field - derived sample
• Calculated = Total Pooled Volume (μl) - Pre-Enriched Library Volume (μl)
Automation

Automation Name

Setting

Value

Specification

Calculate Pre-Enriched Library Volume & RSB Volume

    

Command line

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 (step.::Library Pool Plexity:: == ::1-plex::) {output.::Pre-Enriched Library Volume (uL):: = 14} ; \

if (step.::Library Pool Plexity:: == ::12-plex::) {output.::Pre-Enriched Library Volume (uL):: = 2.5} ; \

output.::RSB Volume (uL):: = step.::Total Pooled Volume (uL):: - output.::Pre-Enriched Library Volume (uL):: ' \

-log {compoundOutputFileLuid0}"

Set Next Step - Hybridize Probes

    

Command line

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 = ::Hybridize Probes (Illumina DNA Prep with Enrichment (S) Tagmentation v1.0)::' \

-log {compoundOutputFileLuid0}"

Next Step

Setting

Value

Start Next Step
• Manual
• Step 9: Hybridize Probes (Illumina DNA Prep with Enrichment (S) Tagmentation) [optional]

Assign Next Step

Automatic

Safe Stopping Point

 

Master Step 7: Qubit (Illumina DNA Prep with Enrichment (S) Tagmentation)

Step Type: Standard QC

Input = Cleaned Up Libraries

Output = Measurement

Placement

Setting

Value

Destination Containers

Tube
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Criteria 1 - Source Data Field

Text

Default: Concentration

 

 

Criteria 1 - Operator

Text

Default: >=
   

Criteria 1 - Threshold Value

Numeric

  
   

Criteria 2 - Source Data Field

Text

Default: Concentration
   

Criteria 2 - Operator

Text

Default: <=
   

Criteria 2 - Threshold Value

Numeric

  

Step File Placeholders

 

File Name

Log

Auto
     

QC Log File

Auto
     

QC Result File

Auto
     

Upload File

Manual

Sample Table

Table Columns

Concentration

Numeric

 

Global field - derived sample
   

Conc. Units

Text

Global field - derived sample
Automation

Automation Name

Setting

Value

Specification

Assign QC Flags

Trigger Location

Record Details

  
 

Trigger Style

Manual Button

  
     

Command line

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 and Copy Concentration

Trigger Location

Record Details

 

 

Trigger Style

Automatic upon exit

 

 

 

 

Command line

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

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Automatic

Safe Stopping Point

 

Master Step 8: Pool Pre-Enriched Libraries - Mass (Illumina DNA Prep with Enrichment (S) Tagmentation)

Step Type: Standard

Input = Diluted Pre-Enriched Libraries

Output = Pooled Pre-Enriched Libraries

Reagent Kits

Kit Name

Supplier

Cat. #

Agencourt AMPure XP purification beads

Beckman Coulter

A63880

Illumina DNA Prep -Tagmentation (S) Beads

Illumina

20025519; 20025520
Placement

Setting

Value

Destination Containers

Tube
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Library Pool

Text

Dropdown
• 1-plex
• 12-plex
   

Pre-Enriched Library Sample (ng)

Numeric
• Read Only
• Default = 500
   

Total Pooled Volume (μl)

Numeric
• Read Only
• Default = 30

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Concentration

Numeric
• Global field - derived sample
• Copied from previous step
   

Conc. Unit

Text
• Global field - derived sample
• Copied from previous step
   

Pre-Enriched Library Volume (μl)

Numeric

Calculated = Pre-Enriched Library Sample (ng) / Concentration
   

RSB Volume (μl)

Numeric

Calculated = Total Pooled Volume (μl) - Pre-Enriched Library Volume (μl)
Automation

Automation Name

Setting

Value

Specification

Copy Concentration

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon entry

  
     

Command line

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.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units::' \

-log {compoundOutputFileLuid0}"

Calculate Pre-Enriched Library Volume & RSB Volume

Trigger Location

Record Details

 
 

Trigger Style

Manual Button

  
     

Command line

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 (step.::Library Pool Plexity:: = 1-plex) {output.::Pre-Enriched Library Volume (uL):: = 14} ; \

if (step.::Library Pool Plexity:: = 12-plex) {output.::Pre-Enriched Library Volume (uL):: = 2.5} ; \

output.::RSB Volume (uL):: = step.::Total Pooled Volume (uL):: - output.::Pre-Enriched Library Volume (uL):: ' \

-log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location

Record Details

 

 

Trigger Style

Automatic upon exit

 

 

 

 

Command line

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}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Automatic

Safe Stopping Point

 

Master Step 9: Hybridize Probes (Illumina DNA Prep with Enrichment (S) Tagmentation)

Input = Pooled Pre-Enriched Libraries

Output = Hybridized Probes

Reagent Kits

Kit Name

Supplier

Cat. #

Illumina DNA Fast Hyb - Enrichment Beads + Buffers

Illumina

20025519; 20025520

Illumina DNA Fast Hyb - Enrichment PCR + Buffers

Illumina

20025519; 20025520

Illumina Exome Panel (8 Enrichment Reactions) (CEX)[optional]

Illumina

20020183

TruSight One (6 Enrichment Reactions) (TOO)[optional]

Illumina

20029227

TruSight One Expanded (6 Enrichment Reactions) (TOE)[optional]

Illumina

20029226

TruSight Cancer (8 Enrichment Reactions)[optional]

Illumina

FC-121-0202

TruSight Hereditary Cancer (8 Enrichment Reactions)[optional]

Illumina

20029551

TruSight Cardio (8 Enrichment Reactions)[optional]

Illumina

20029229

TruSeq Neurodegeneration (8 Enrichment Reactions)[optional]

Illumina

20029550

Illumina Custom Enrichment Panel via DesignStudio (8 Enrichment Reactions)[optional]

Illumina

20025371
Placement

Setting

Value

Destination Containers

96 well plate
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Thermal Cycler Program

Text

Default: NF-HYB program
   

PCR Cycles

Numeric

 

Step File Placeholders

 

File Name

Log

Auto
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Advance

Trigger Location

Record Details

 

 

Trigger Style

Automatic upon exit

 

 

 

 

Command line

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}"

Next Step

Setting

Value

Start Next Step

Automatic

Assign Next Step

Automatic

Must move forward

 

Master Step 10: Capture Hybridize Probes (Illumina DNA Prep with Enrichment (S) Tagmentation)

Step Type: Standard

Input = Pooled Pre-Enriched Libraries

Output = Hybridized Probes

Reagent Kits

Kit Name

Supplier

Cat. #

Illumina DNA Fast Hyb - Enrichment PCR + Buffers

Illumina

20025519; 20025520

Illumina DNA Fast Hyb - Enrichment Beads + Buffers

Illumina

20025519; 20025520

Illumina Exome Panel (8 Enrichment Reactions) (CEX)[optional]

Illumina

20020183

TruSight One (6 Enrichment Reactions) (TOO)(optional)[optional]

Illumina

20029227

TruSight One Expanded (6 Enrichment Reactions) (TOE)[optional]

Illumina

20029226

TruSight Cancer (8 Enrichment Reactions)[optional]

Illumina

FC-121-0202

TruSight Hereditary Cancer (8 Enrichment Reactions)[optional]

Illumina

20029551

TruSight Cardio (8 Enrichment Reactions)[optional]

Illumina

20029229

TruSeq Neurodegeneration (8 Enrichment Reactions)[optional]

Illumina

20029550

Illumina Custom Enrichment Panel via DesignStudio (8 Enrichment Reactions)[optional]

Illumina

20025371
Placement

Setting

Value

Destination Containers

96 well plate or tube
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Total Samples

Numeric
• Default = 0
• Calculated = Total Samples + 1
   

EE1 (μl)

Numeric

Calculated = Total Samples * 28.5 * 1.1
   

HP3 (μl)

Numeric

Calculated = Total Samples * 1.5 *1.1

Step File Placeholders

 

File Name

Log

Auto
Automation

Automation Name

Setting

Value

Specification

Calculate Total Samples and Calculate Master Mix

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon entry

  
     

Command line

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 Samples:: = step.::Total 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 'step.::EE1 (uL):: = step.::Total Samples:: * 1.1 * 28.5 ; \

step.::HP3 (uL):: = step.::Total Samples:: * 1.1 * 1.5 ;' \

-log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location

Record Details

 

 

Trigger Style

Automatic upon exit

 

 

 

 

Command line

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}"

Next Step

Setting

Value

Start Next Step

Automatic

Assign Next Step

Automatic

Must move forward

 

Master Step 11: Amplify Enriched Library (Illumina DNA Prep with Enrichment (S) Tagmentation)

Step Type: Standard

Input = Pooled Pre-Enriched Libraries

Output = Hybridized Probes

Reagent Kits

Kit Name

Supplier

Cat. #

Illumina DNA Fast Hyb - Enrichment PCR + Buffers

Illumina

20025519; 20025520
Placement

Setting

Value

Destination Containers

96 well plate or tube
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Thermal Cycler Program

Text

Default = AMP
   

PCR Cycles

Numeric

 

Step File Placeholders

 

File Name

Log

Auto
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Advance

Trigger Location

Record Details

 

 

Trigger Style

Automatic upon exit

 

 

 

 

Command line

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}"

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Automatic

Safe Stopping Point

 

Master Step 12: Clean Up Amplified Enriched Library (Illumina DNA Prep with Enrichment (S) Tagmentation)

Input = Amplified enriched libraries

Output = Cleaned up amplified enriched libraries

Reagent Kits

Kit Name

Supplier

Cat. #

Agencourt AMPure XP beads, 5 ml

Beckman Coulter

A63880

Illumina DNA Prep -Tagmentation (S) Beads

Illumina

20025519; 20025520
Placement

Setting

Value

Destination Containers

96 well plate or tube
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

80% EtOH Prep Date

Date

  

Step File Placeholders

 

File Name

Log

 
Automation

Automation Name

Setting

Value

Specification

Set Next Step - Advance

Trigger Location

Record Details

 

 

Trigger Style

Automatic upon exit

 

 

 

 

Command line

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}"

Safe Stopping Point