Illumina Preset Protocol - AmpliSeq for Illumina Comprehensive Cancer Panel

The AmpliSeq for Illumina Comprehensive Cancer Panel includes the following functionality:

• Preconfigured AmpliSeq for Illumina Comprehensive Cancer Panel protocol that supports the preparation of up to 96 uniquely indexed libraries of genomic DNA using the AmpliSeq for Illumina workflow.
• 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: Library Prep (AmpliSeq for Illumina Comprehensive Cancer Panel)

Master Step 1: Dilute DNA (AmpliSeq for Illumina)

Step Type: Standard

Input = DNA with concentration

Output = Diluted DNA (2-200 ng)

Reagent Kits

Kit Name

Supplier

Cat. #

AmpliSeq Library PLUS for Illumina

Illumina

24 - 20019101; 96 - 200191102; 384 - 200191103
Placement

Setting

Value

Specification

Destination Containers

Tube

Configured on step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Desired Concentration (ng/µl)

Numeric

Range = 20–50
 

Multiline Text Fields

Directions

Multiline Text

Preset

Read Only

• If enough DNA is available, dilute to intermediate concentration ~20–50 ng/µl.

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Concentration

Numeric

Global field - derived sample
   

Conc. Units

Text

Global field - derived sample
   

Input Amount (ng)

Numeric

Global field - derived sample
   

Low TE (µl)

Numeric

Global field - derived sample
   

Sample Volume (µl)

Numeric

Global field - derived sample
   

Total Volume (µl)

Numeric

Global field - derived sample
Automation

Automation Name

Setting

Value

Specification

Copy Concentration and Set Sample Volume

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:: ; output.::Sample Volume (uL):: = 5' \-log {compoundOutputFileLuid0}["]

Calculate Input Amount

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 true \-h false \-exp 'output.::Total Volume (uL):: = (output.::Concentration::/step.::Desired Concentration (ng/uL)::) * output.::Sample Volume (uL):: ; \output.::Low TE (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \output.::Input Amount (ng):: = step.::Desired Concentration (ng/uL):: * output.::Sample Volume (uL):: ' \-log {compoundOutputFileLuid0}["]

Next Step

Setting

Value

Start Next Step

Automatic

Assign Next Step

Manual

Must move forward

Optional

• Qubit (AmpliSeq for Illumina Comprehensive Cancer Panel)
• Amplify Targets Replicates (AmpliSeq for Illumina Comprehensive Cancer Panel)

Master Step 2: Qubit (AmpliSeq for Illumina)

Step Type: Standard QC

Input = Diluted DNA ()

Output = Measurement

Placement

Setting

Value

Specification

Destination Containers

Tube

Configured on step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Criteria 1 - Source Data Field

Text

Preset

• Concentration
   

Criteria 1 - Operator

Text

Preset

• >=
   

Criteria 1 - Threshold Value

Numeric

 
   

Criteria 2 - Source Data Field

Text

Preset

• Concentration
   

Criteria 2 - Operator

Text

Preset

• <=
   

Criteria 2 - Threshold Value

Numeric

 

Step File Placeholders

 

File Name

Log

Auto
     

QC Log File

Auto
     

QC Result File

Manual
     

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

Automatic

Assign Next Step

Automatic

Must move forward

 

Master Step 3: Dilute DNA (AmpliSeq for Illumina)

Step Type: Standard

Input = DNA with concentration (4–400 ng)

Reagent Kits

Kit Name

Supplier

Cat. #

AmpliSeq Library PLUS for Illumina

Illumina

24 - 20019101; 96 - 200191102; 384 - 200191103
Placement

Setting

Value

Specification

Destination Containers

1.5 mL Tube

Configured on step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Desired Concentration (ng/µl)

Numeric

Range = 20–50

Step File Placeholders

 

File Name

Log

Auto

 

Sample Table

Table Columns

Concentration

Numeric

Global field - derived sample
   

Conc. Units

Text

Global field - derived sample
   

Input Amount (ng)

Numeric

Global field - derived sample
   

Low TE (µl)

Numeric

Global field - derived sample
   

Sample Volume (µl)

Numeric

Global field - derived sample
   

Total Volume (µl)

Numeric

Global field - derived sample
Automation

Automation Name

Setting

Value

Specification

Copy Concentration and Set Sample Volume

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:: ; output.::Sample Volume (uL):: = 5' \-log {compoundOutputFileLuid0}["]

Calculate Input Amount

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 true \-h false \-exp 'output.::Total Volume (uL):: = (output.::Concentration::/step.::Desired Concentration (ng/uL)::) * output.::Sample Volume (uL):: ; \output.::Low TE (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \output.::Input Amount (ng):: = step.::Desired Concentration (ng/uL):: * output.::Sample 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

Automatic

• Amplify Targets (AmpliSeq for Illumina Comprehensive Cancer Panel)

Assign Next Step

Automatic

Must move forward

 

Master Step 4: Amplify Targets Replicates (AmpliSeq for Illumina)

(This is the Drop-down text)

Step Type: Standard

Input = Diluted DNA (4–400 ng)

4x replicates

Amplified DNA

Derived Sample Generation: Fixed = ["]4["]

Reagent Kits

Kit Name

Supplier

Cat. #

AmpliSeq Library PLUS for Illumina

Illumina

24 - 20019101; 96 - 200191102; 384 - 200191103

AmpliSeq Comprehensive Cancer Panel for Illumina

Illumina

20019160
Placement

Setting

Value

Specification

Destination Containers

96 well plate

Configured on step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

20x AmpliSeq Sample ID Panel For Illumina

Toggle Switch

  
   

20x AmpliSeq Sample ID Panel For Illumina

Text

  
   

Thermal Cycler Program

Text

Preset

• AMP_CCP
   

PCR Cycles

Numeric

  
   

Group of PresetsCCP

    
   

Thermal Cycler Program = AMP_CCP

    
   

Instructions

Multiline Text

Preset

• Add 5 µl 2X AmpliSeq Comprehensive Cancer Panel Pool 1 (blue cap) to the first well, and 5 µl 2X AmpliSeq Comprehensive Cancer Panel Pool 2 (blue cap) to the second.Add 5 µl 2X AmpliSeq Comprehensive Cancer Panel Pool 3 (blue cap) to the third well, and 5 µl 2XAmpliSeq Comprehensive Cancer Panel Pool 4 (blue cap) to the fourth.

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

5X AmpliSeq HiFi Mix (µl)

Numeric

Global field - derived sample
   

DNA Volume (µl)

Numeric
• Global field - derived sample
• Calculated based on concentration from previous step
   

Concentration

Numeric

Global field - derived sample
   

Conc. Units

Text

Global field - derived sample
   

Nuclease-free water (µl)

Numeric
• Global field - derived sample
• Calculated
   

Prep Input Volume (µl)

Numeric
• Global field - derived sample
• Calculated
   

Prep Input Amount (ng)

Numeric

Required

• Global field - derived sample
• User input
• 4–400
Automation

Automation Name

Setting

Value

Specification

Copy Concentration, Total Volume and Input Amount - CCP

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:: ; output.::Total Volume (uL):: = input.::Total Volume (uL):: ; output.::Input Amount (ng):: = input.::Input Amount (ng):: ; output.::5X AmpliSeq HiFi Mix (uL):: = 9.0'\-log {compoundOutputFileLuid0}["]

Calculate Prep Input

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 'output.::Prep Input Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Concentration:: ; \if (output.::Prep Input Volume (uL):: < 13.5) {output.::Nuclease-free water (uL):: = 13.5 - output.::Prep Input 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 5: Partially Digested Amplicons with Pooling (AmpliSeq for Illumina)

Step Type: Pooling

Input = Amplified DNA

Output = Pooled Partially Digested Amplicons

Pooling Settings = Label Uniqueness = Off

Reagent Kits

Kit Name

Supplier

Cat. #

AmpliSeq Library PLUS for Illumina

Illumina

24 - 20019101; 96 - 200191102; 384 - 200191103
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Thermal Cycler Program

Text

Preset

• FUPA

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 6: Ligate Indexes (AmpliSeq for Illumina CCP)

(This is the Drop-down text)

Step Type: Standard

Input = Partially Digested Amplicons

Output = Ligated Libraries

Add Labels

Reagent Kits

Kit Name

Supplier

AmpliSeq Library PLUS for Illumina

  
Placement

Setting

Value

Specification

Destination Containers

96 well plate

Configured on step
Add Labels

Setting

Value

Label Groups

AmpliSeq CD Indexes Set A for Illumina - AmpliSeq CD Indexes Set A for Illumina-label-sheet.xlsx
 

AmpliSeq CD Indexes Set B for Illumina - AmpliSeq CD Indexes Set B for Illumina-label-sheet.xlsx
 

AmpliSeq CD Indexes Set C for Illumina - AmpliSeq CD Indexes Set C for Illumina-label-sheet.xlsx
 

AmpliSeq CD Indexes Set D for Illumina - AmpliSeq CD Indexes Set D for Illumina-label-sheet.xlsx
 

AmpliSeq UD Indexes for Illumina (24 Indexes) - AmpliSeq UD Indexes for Illumina (24 Indexes)-label-sheet.xlsx
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Thermal Cycler Program

Text

Preset

• LIGATE

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

AmpliSeq Workflow

Text

Required

• Global field - derived sample
• Standard Workflow or Equalizer Workflow (preset)
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}["]

Route AmpliSeq Samples - CCP

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 'AmpliSeq Workflow' \

--FIELD_VALUE 'Standard Workflow' \

--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Comprehensive Cancer Panel v1.0' \

--STEP 'Clean Up Library (AmpliSeq for Illumina Comprehensive Cancer Panel v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS' \

\

--FIELD_NAME 'AmpliSeq Workflow' \

--FIELD_VALUE 'Equalizer Workflow' \

--WORKFLOW 'Equalizer AmpliSeq for Illumina Comprehensive Cancer Panel v1.0' \

--STEP 'Clean Up Library (AmpliSeq for Illumina Comprehensive Panel v1.0)' \

--INPUTS_OR_OUTPUTS 'OUTPUTS'["]

Next Step

Setting

Value

Start Next Step

Manual

Assign Next Step

Automatic

Safe Stopping Point

 

Protocol 2: Standard Workflow (AmpliSeq for Illumina Comprehensive Cancer Panel)

Master Step 1: Clean Up Library (AmpliSeq for Illumina)

(This is the Drop-down text)

Step Type: No output

Input = Ligated Libraries

Output = Cleaned Up Libraries

Reagent Kits

Kit Name

Supplier

Cat. #

Agencourt AMPure XP Beads

Thermo

NC9959336; NC9933872
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

70% 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

Automatic

Assign Next Step

Automatic

Must move forward

 

Master Step 2: Amplify Library (AmpliSeq for Illumina)

Step Type: No Output

Input = Cleaned Up Libraries

Output = Amplified Libraries

Reagent Kits

Kit Name

Supplier

Cat. #

Agencourt AMPure XP Beads

Thermo

NC9959336; NC9933872

AmpliSeq Library PLUS for Illumina

Illumina

24 - 20019101; 96 - 200191102; 384 - 200191103
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Thermal Cycler Program

Text

Group of Defaults

• Standard Workflow
– AMP_7
   

Total Samples

Numeric

Preset

• 0
   

1X Lib AMP Mix (µl)

Numeric

  
   

10X Library Amp Primers (µl)

Numeric

  

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.::1X Lib Amp Mix:: = step.::Total Samples:: * 1.1 * 45 ; \step.::10X Library Amp Primers:: = step.::Total Samples:: * 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

Manual

Assign Next Step

Automatic

Safe Stopping Point

 

Master Step 3: Perform Second Clean Up (AmpliSeq for Illumina)

Step Type: Standard

Input = Amplified Libraries

Output = Cleaned Up Amplified Libraries

Reagent Kits

Kit Name

Supplier

Cat. #

Agencourt AMPure XP Beads

Thermo

NC9959336; NC9933872

AmpliSeq Library PLUS for Illumina

Illumina

24 - 20019101; 96 - 200191102; 384 - 200191103
Placement

Setting

Value

Specification

Destination Containers

96 well plate

Configured on step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

70% 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}["]

End of standard protocol

Protocol 3: Equalizer Workflow (AmpliSeq for Illumina Comprehensive Cancer Panel)

Master Step 1: Clean Up Library (AmpliSeq for Illumina)

Step Type: No Output

Input = Ligated Libraries

Output = Cleaned Up Libraries

Reagent Kits

Kit Name

Supplier

Cat. #

Agencourt AMPure XP Beads

Thermo

NC9959336; NC9933872
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

70% 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

Automatic

Assign Next Step

Automatic

Must move forward

 

Master Step 2: Amplify Library (AmpliSeq for Illumina)

Step Type: No Output

Input = Cleaned Up Libraries

Output = Amplified Libraries

Reagent Kits

Kit Name

Supplier

Cat. #

Agencourt AMPure XP Beads

Thermo

NC9959336; NC9933872

AmpliSeq Library PLUS for Illumina

Illumina

24 - 20019101; 96 - 200191102; 384 - 200191103
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Thermal Cycler Program

Text

Group of Defaults

• Equalizer Workflow
– EQUAL
   

Total Samples

Numeric
• 0 (preset)
• Calculated
   

1X Lib AMP Mix (µl)

Numeric

Calculated
   

10X Library Amp Primers (µl)

Numeric

Calculated

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.::1X Lib Amp Mix:: = step.::Total Samples:: * 1.1 * 45 ; \step.::10X Library Amp Primers:: = step.::Total Samples:: * 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 3: Perform Capture and Clean Up (AmpliSeq for Illumina)

Step Type: Standard

Input = Amplified Libraries

Output = Cleaned Up Libraries

Place Samples = 96 well plate

Reagent Kits

Kit Name

Supplier

Cat.#

AmpliSeq Library Equalizer for Illumina

Illumina

20019171
Placement

Setting

Value

Specification

Destination Containers

96 well plate

Configured on step
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 4: Elute Library (AmpliSeq for Illumina)

Step Type: Standard

Input = Cleaned Up Libraries

Output = Final Library

Reagent Kits

Kit Name

Supplier

Cat. #

AmpliSeq Library Equalizer for Illumina

Illumina

20019171
Placement

Setting

Value

Specification

Destination Containers

96 well plate

Configured on step
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

Thermal Cycler Program

Text

Preset

• ELUTE

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}["]

End of Equalizer Protocol