# Illumina DNA Prep with Enrichment (S) Tagmentation v1.2 ## Protocol 1: Prep Sample (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) Protocol Type = Sample Prep **Next Steps Configuration**

### Step 1: Sort Sample (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Master Step Name = Sort Sample (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Step Type = No Outputs #### Automations

Sort & Set Next Step

* Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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 v1.2):: } ; \ if (input.::NFE Sample Type:: == ::Saliva:: ) {nextStep=::Saliva Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2):: } ; \ if (input.::NFE Sample Type:: == ::gDNA:: ) {nextStep=::Qubit gDNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2):: } ; \ if (input.::NFE Sample Type:: == ::FFPE DNA::) {nextStep=::Qubit FFPE DNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2):: }' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}

Presets

Blood
Saliva
gDNA
FFPE DNA

| | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 2: Blood Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Master Step Name = Blood Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * Agencourt AMPure XP beads, 5 ml * Supplier = Beckman Coulter * Catalog Number = A63880 * Website = [www.beckman.com](https://help.connected.illumina.com/clarity-lims/library-prep/targeted-enrichment/www.beckman.com) * Flex Lysis Reagent Kit * Supplier = Illumina * Catalog Number = 20015884 * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/targeted-enrichment/www.illumina.com) #### Automations

Calculate Total Samples & Master Mix

Set Next Step - Remove

Route NFE - Blood

* Trigger Location = Step * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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 v1.2' \ --STEP 'Tagment Genomic DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' " ``` {% endcode %} > ℹ The version of the workflow and step for the routing script may be different depending on the version of IPP installed.

#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ---------------------- | -------------- | ----------- | ----------------------------------------- | | 80% EtOH Prep Date | Date | | | | BLB (uL) | Numeric | | Decimal Places Displayed = 2 | | PK1 (uL) | Numeric | | Decimal Places Displayed = 2 | | Thermal Cycler Program | Text | | Default = BLP | | Total Samples | Numeric | | Default = 0 | | Water (uL) | Numeric | | Decimal Places Displayed = 2 | * Step File Placeholders * Log - Automatically attached * Sample Table * Sample Display Default = Collapse * Well Sort Order = Row * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 3: Saliva Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Master Step Name = Saliva Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * Agencourt AMPure XP, 5 ml * Supplier = Beckman Coulter * Catalog Number = A63880 #### Automations

Copy NFE Sample Type and Set UDFs

Set Next Step - Remove

Route NFE - Saliva

* Trigger Location = Step * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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 v1.2' \ --STEP 'Tagment Genomic DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' " ``` {% endcode %} > ℹ The version of the workflow and step for the routing script may be different depending on the version of IPP installed.

Presets

Blood
Saliva
gDNA
FFPE DNA

| | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Sample Volume (uL) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Water for Resuspension (uL) | Numeric | | Default = 30 | | Project | Project Name | Built-in | | | ### Step 4: Qubit gDNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Master Step Name = Qubit gDNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Step Type = Standard QC * Measurement Generation = Fixed, 1 * Naming Convention = {InputItemName} #### Automations

Assign QC flags

* Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} \ script:assignQC \ -i {processURI:v2} \ -log {compoundOutputFileLuid1} \ -qcResult {compoundOutputFileLuid2}" ``` {% endcode %}

Set Next Step and Copy Concentration

#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------------------ | -------------- | ----------- | ----------------------------------------- | | Criteria 1 - Operator | Text | | Default = >= | | Criteria 1 - Source Data Field | Text | | Default = Concentration | | Criteria 1 - Threshold Value | Numeric | | | | Criteria 2 - Operator | Text | | Default = <= | | Criteria 2 - Source Data Field | Text | | Default = Concentration | | Criteria 2 - Threshold Value | Numeric | | | * Step File Placeholders * Log - Automatically attached * QC Log File - Automatically attached * QC Result File - Automatically attached * Upload File - Manually uploaded * Sample Table * Enable QC Flags = Yes * Sample Display Default = Expand * Well Sort Order = Row * File Column Options * File Column Display = Show * File Attachment Method = Manual * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | -------------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Concentration | Numeric | Required Field | Decimal Places Displayed = 2 | | Derived Sample | Conc. Units | Text | Required Field | | | Derived Sample | Sample Name | Built-in | | | | Measurement | Concentration | Numeric | | Decimal Places Displayed = 2 | | Measurement | Conc. Units | Text | | | | Project | Project Name | Built-in | | | ### Step 5: Dilute gDNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Master Step Name = Dilute gDNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} #### Automations

Copy Concentration

Calculate Dilution Volume & Sample Volume

* Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup 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.hasValue(::Conc. Units::) || output.::Conc. Units:: != ::ng/uL::) { fail(::This automation expects Conc. Units to be ng/uL.::) ; };\ output.::Sample Volume (uL):: = (step.::Desired gDNA Concentration (ng/uL):: * step.::Total Volume (uL)::) / output.::Concentration::;\ output.::Dilution Volume (uL):: = step.::Total Volume (uL):: - output.::Sample Volume (uL)::;\ output.::Final Concentration:: = step.::Desired gDNA Concentration (ng/uL)::;' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}

Set Next Step - Remove & Copy NFE Sample Type

Route NFE - gDNA

* Trigger Location = Step * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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 v1.2' \ --STEP 'Tagment Genomic DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' " ``` {% endcode %} > ℹ The version of the workflow and step for the routing script may be different depending on the version of IPP installed.

Presets

RSB
10 mM Tris-HCI, pH 7.5–8.5

| | Total Volume (uL) | Numeric | | Decimal Places Displayed = 2 | * Step File Placeholders * Log - Automatically attached * Sample Table * Sample Display Default = Expand * Well Sort Order = Row * File Column Options * File Column Display = Show * File Attachment Method = Manual * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------------- | -------------- | -------------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Concentration | Numeric | Required Field | Decimal Places Displayed = 2 | | Derived Sample | Conc. Units | Text | Required Field | | | Derived Sample | Dilution Volume (uL) | Numeric | | | | Derived Sample | Final Concentration | Numeric | Required Field | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Sample Volume (uL) | Numeric | | Decimal Places Displayed = 2 | | Project | Project Name | Built-in | | | ### Step 6: Qubit FFPE DNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Master Step Name = Qubit FFPE DNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Step Type = Standard QC * Measurement Generation = Fixed, 1 * Naming Convention = {InputItemName} #### Automations

Assign QC flags

* Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} \ script:assignQC \ -i {processURI:v2} \ -log {compoundOutputFileLuid1} \ -qcResult {compoundOutputFileLuid2}" ``` {% endcode %}

Set Next Step and Copy Concentration

#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------------------ | -------------- | ----------- | ----------------------------------------- | | Criteria 1 - Operator | Text | | Default = >= | | Criteria 1 - Source Data Field | Text | | Default = Concentration | | Criteria 1 - Threshold Value | Numeric | | | | Criteria 2 - Operator | Text | | Default = <= | | Criteria 2 - Source Data Field | Text | | Default = Concentration | | Criteria 2 - Threshold Value | Numeric | | | * Step File Placeholders * Log - Automatically attached * QC Log File - Automatically attached * QC Result File - Automatically attached * Upload File - Manually uploaded * Sample Table * Enable QC Flags = Yes * Sample Display Default = Expand * Well Sort Order = Row * File Column Options * File Column Display = Show * File Attachment Method = Manual * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | -------------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Concentration | Numeric | Required Field | Decimal Places Displayed = 2 | | Derived Sample | Conc. Units | Text | Required Field | | | Derived Sample | Sample Name | Built-in | | | | Measurement | Concentration | Numeric | | Decimal Places Displayed = 2 | | Measurement | Conc. Units | Text | | | | Project | Project Name | Built-in | | | ### Step 7: Dilute FFPE DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Master Step Name = Dilute FFPE DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} #### Automations

Copy Concentration

Calculate Dilution Volume & Sample Volume

* Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup 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.hasValue(::Conc. Units::) || output.::Conc. Units:: != ::ng/uL::) { fail(::This automation expects Conc. Units to be ng/uL.::) ; };\ output.::Sample Volume (uL):: = (step.::Desired gDNA Concentration (ng/uL):: * step.::Total Volume (uL)::) / output.::Concentration::;\ output.::Dilution Volume (uL):: = step.::Total Volume (uL):: - output.::Sample Volume (uL)::;\ output.::Final Concentration:: = step.::Desired gDNA Concentration (ng/uL)::;' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}

Set Next Step - Advance & Copy NFE Sample Type

Presets

RSB
10 mM Tris-HCI, pH 7.5–8.5

| | Total Volume (uL) | Numeric | | Decimal Places Displayed = 2 | * Step File Placeholders * Log - Automatically attached * Sample Table * Sample Display Default = Expand * Well Sort Order = Row * File Column Options * File Column Display = Show * File Attachment Method = Manual * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------------- | -------------- | -------------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Concentration | Numeric | Required Field | Decimal Places Displayed = 2 | | Derived Sample | Conc. Units | Text | Required Field | | | Derived Sample | Dilution Volume (uL) | Numeric | | | | Derived Sample | Final Concentration | Numeric | Required Field | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Sample Volume (uL) | Numeric | | Decimal Places Displayed = 2 | | Project | Project Name | Built-in | | | ## Protocol 2: Library Prep (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) Protocol Type = Library Prep **Next Steps Configuration**

### Step 1: Tagment Genomic DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Master Step Name = Tagment Genomic DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * Illumina DNA Prep -Tagmentation (S) Beads * Supplier = Illumina * Catalog Number = 20025519; 20025520 * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/targeted-enrichment/www.illumina.com) * Illumina DNA/RNA Prep - Tagmentation PCR Reagents * Supplier = Illumina * Catalog Number = 20025519; 20025520 * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/targeted-enrichment/www.illumina.com) #### Automations

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

* Trigger Location = Record Details * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup 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(::Final Concentration::)) {output.::Concentration:: = input.::Final Concentration:: ; output.::Conc. Units:: = input.::Conc. Units::}' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}

Calculate Sample Volume & Water

* Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}

Set Next Step - Advance

Default =
Choose the preheat lid option and set to 100C
Set the reaction volume to 50 uL
55C for 5 minutes
Hold at 10C

| | Thermal Cycler Program | Text | | Default = TAG | | Total Samples | Numeric | | Default = 0 | | Total Volume (uL) | Numeric | | Default = 30 | * Step File Placeholders * Log - Automatically attached * Sample Table * Sample Display Default = Expand * Well Sort Order = Row * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------------- | -------------- | -------------- | ---------------------------------------------------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Concentration | Numeric | Required Field | Decimal Places Displayed = 2 | | Derived Sample | Conc. Units | Text | Required Field | | | Derived Sample | Desired Input Amount (ng) | Numeric | | | | Derived Sample | NFE Sample Type | Text Dropdown | Required Field |

Presets

Blood
Saliva
gDNA
FFPE DNA

| | Derived Sample | Nuclease-free water (uL) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Sample Volume (uL) | Numeric | | Decimal Places Displayed = 2 | | Project | Project Name | Built-in | | | ### Step 2: Post Tagmentation Cleanup (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Master Step Name = Post Tagmentation Cleanup (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Step Type = No Outputs * Reagent Kits * Illumina DNA/RNA Prep - Tagmentation Buffers * Supplier = Illumina * Catalog Number = 20025519; 20025520 * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/targeted-enrichment/www.illumina.com) #### Automations

Set Next Step - Advance

Presets

Blood
Saliva
gDNA
FFPE DNA

| | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 3: Amplify Tagmented DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Master Step Name = Amplify Tagmented DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Step Type = Add Labels * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * Illumina DNA Fast Hyb - Enrichment PCR + Buffers * Supplier = Illumina * Catalog Number = 20025519; 20025520 * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/targeted-enrichment/www.illumina.com) #### Automations

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

* Trigger Location = Record Details * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup 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.::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 (ng):: >= 10 && input.::Desired Input Amount (ng):: <= 49) {output.::PCR Cycles:: = 12}} ; \ if (output.::NFE Sample Type:: == ::gDNA::) {if (input.::Desired Input Amount (ng):: >= 50 && input.::Desired Input Amount (ng):: <= 1000) {output.::PCR Cycles:: = 9}} ; \ if (output.::NFE Sample Type:: == ::FFPE DNA::) {if (input.::Desired Input Amount (ng):: >= 50 && input.::Desired Input Amount (ng):: <= 1000) {output.::PCR Cycles:: = 12}}' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}

Set Next Step - Advance

#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Placement = Enabled * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Placement Pattern = Row * Destination Containers * 96 well plate #### Add Labels * Label Groups * IDT for Illumina DNA-RNA UD Indexes Set A Tagmentation * IDT for Illumina DNA-RNA UD Indexes Set A-D Tagmentation * IDT for Illumina DNA-RNA UD Indexes Set B Tagmentation * IDT for Illumina DNA-RNA UD Indexes Set C Tagmentation * IDT for Illumina DNA-RNA UD Indexes Set D Tagmentation * Illumina DNA-RNA UD Indexes Set A B C D Tagmentation * Illumina DNA-RNA UD Indexes Set A Tagmentation * Illumina DNA-RNA UD Indexes Set B Tagmentation * Illumina DNA-RNA UD Indexes Set C Tagmentation * Illumina DNA-RNA UD Indexes Set D Tagmentation #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ----------------------------------- | -------------- | ----------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | EPM (uL) | Numeric | | | | Nuclease-free water (uL) | Numeric | | | | Thermal Cycler Program | Text | | Default = eBLT PCR | | Thermal Cycler Program Instructions | Multiline Text | |

Default =
Choose the preheat lid option and set to 100°C Set the reaction volume to 50 uL
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

| | Total Samples | Numeric | | Default = 0 | * Step File Placeholders * Log - Automatically attached * Sample Table * Sample Display Default = Expand * Well Sort Order = Row * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | -------------- | ---------------------------------------------------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | NFE Sample Type | Text Dropdown | Required Field |

Presets

Blood
Saliva
gDNA
FFPE DNA

| | Derived Sample | PCR Cycles | Numeric | | Decimal Places Displayed = 0 | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 4: Clean Up Libraries (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Master Step Name = Clean Up Libraries (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * Agencourt AMPure XP Beads * Supplier = Thermo * Catalog Number = NC9959336; NC9933872 * Illumina DNA Prep -Tagmentation (S) Beads * Supplier = Illumina * Catalog Number = 20025519; 20025520 * Website = [illumina.com](https://github.com/illumina-swi/clarity-int-docs/blob/main/docs/int/ipp/other/illumina.com) #### Automations

Set Next Step - Advance

#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------ | -------------- | ----------- | ----------------------------------------- | | 80% EtOH Prep Date | Date | | | * Step File Placeholders * Log - Automatically attached * Sample Table * Sample Display Default = Expand * Well Sort Order = Row * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 5: Bioanalyzer QC Qualify Pre-Enriched Libraries (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Master Step Name = Bioanalyzer QC Qualify Pre-Enriched Libraries (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Step Type = Standard QC * Measurement Generation = Fixed, 1 * Naming Convention = {InputItemName} #### Automations

Generate Bioanalyzer driver file

* Trigger Location = Record Details * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar -u {username} -p {password} \ script:driver_file_generator \ -i {processURI:v2} \ -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 -u {username} -p {password} \ script:addBlankLines \ -i {stepURI:v2} \ -f {compoundOutputFileLuid0}.csv \ -l {compoundOutputFileLuid1} \ -sep COMMA \ -b ',False,' \ -h 1 \ -c LIMSID \ -pre 'Sample '" ``` {% endcode %}

Parse Bioanalyzer XML and assign QC flags

* BioAnalyzer DNA 1000 Chip

#### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------------------------------- | -------------- | ----------- | ----------------------------------------- | | Criteria 1 - Operator | Text | | Default = >= | | Criteria 1 - Source Data Field | Text | | Default = Peak 2 Size - bp | | Criteria 1 - Threshold Value | Numeric | | Default = 300 | | Criteria 2 - Operator | Text | | Default = <= | | Criteria 2 - Source Data Field | Text | | Default = Peak 2 Size - bp | | Criteria 1 - Threshold Value | Numeric | | Default = 400 | | Use strict matching for Bioanalyzer results | Toggle Switch | | Default = None Set | * Step File Placeholders * Bioanalyzer Input File - Automatically attached * Bioanalyzer Input File Generation Log File - 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 = Show * File Attachment Method = Manual * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Measurement | A260/280 ratio | Numeric | | Decimal Places Displayed = 2 | | Measurement | Number of Peaks found | Numeric | | Decimal Places Displayed = 0 | | Measurement | Number of Regions found | Numeric | | Decimal Places Displayed = 0 | | Measurement | Peak 1 % Integrated Area | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 1 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 1 Molarity | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 1 MW | Numeric | | Decimal Places Displayed = 0 | | Measurement | Peak 1 Size - bp | Numeric | | Decimal Places Displayed = 0 | | Measurement | Peak 2 % Integrated Area | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 2 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 2 Molarity | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 2 MW | Numeric | | Decimal Places Displayed = 0 | | Measurement | Peak 2 Size - bp | Numeric | | Decimal Places Displayed = 0 | | Measurement | Peak 3 % Integrated Area | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 3 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 3 Molarity | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 3 MW | Numeric | | Decimal Places Displayed = 0 | | Measurement | Peak 3 Size - bp | Numeric | | Decimal Places Displayed = 0 | | Measurement | Peak 4 % Integrated Area | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 4 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 4 Molarity | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 4 MW | Numeric | | Decimal Places Displayed = 0 | | Measurement | Peak 4 Size - bp | Numeric | | Decimal Places Displayed = 0 | | Measurement | Peak 5 % Integrated Area | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 5 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 5 Molarity | Numeric | | Decimal Places Displayed = 2 | | Measurement | Peak 5 MW | Numeric | | Decimal Places Displayed = 0 | | Measurement | Peak 5 Size - bp | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 1 % of Total | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 1 Average Size - bp | Numeric | | Decimal Places Displayed = 0 | | Measurement | Region 1 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 1 Molarity | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 2 % of Total | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 2 Average Size - bp | Numeric | | Decimal Places Displayed = 0 | | Measurement | Region 2 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 2 Molarity | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 3 % of Total | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 3 Average Size - bp | Numeric | | Decimal Places Displayed = 0 | | Measurement | Region 3 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 3 Molarity | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 4 % of Total | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 4 Average Size - bp | Numeric | | Decimal Places Displayed = 0 | | Measurement | Region 4 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 4 Molarity | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 5 % of Total | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 5 Average Size - bp | Numeric | | Decimal Places Displayed = 0 | | Measurement | Region 5 Conc. | Numeric | | Decimal Places Displayed = 2 | | Measurement | Region 5 Molarity | Numeric | | Decimal Places Displayed = 2 | | Measurement | Sample Comment | Text | | | | Project | Project Name | Built-in | | | ### Step 6: Pool Pre-Enriched Libraries - Volume (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Master Step Name = Pool Pre-Enriched Libraries (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Step Type = Pooling * Aliquot Generation = Fixed, 1 * Naming Convention = {PoolName} * Reagent Kits * Agencourt AMPure XP Beads * Supplier = Thermo * Catalog Number = NC9959336; NC9933872 * Illumina DNA Prep -Tagmentation (S) Beads * Supplier = Illumina * Catalog Number = 20025519; 20025520 * Website = [illumina.com](https://github.com/illumina-swi/clarity-int-docs/blob/main/docs/int/ipp/other/illumina.com) #### Automations

Calculate Pre-Enriched Library Volume & RSB Volume

* Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}

Set Next Step - Hybridize Probes

Required Field
Custom Entries

Presets

1-plex
12-plex

| | Total Pooled Volume (uL) | Numeric |

Read Only

| Default = 30 | * Step File Placeholders * Log - Automatically attached * Sample Table * Sample Display Default = Expand * Well Sort Order = Row * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Pre-Enriched Library Volume (uL) | Numeric | | | | Derived Sample | RSB Volume (uL) | Numeric | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 7: Qubit (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Master Step Name = Qubit (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Step Type = Standard QC * Measurement Generation = Fixed, 1 * Naming Convention = {InputItemName} #### Automations

Assign QC flags

* Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} \ script:assignQC \ -i {processURI:v2} \ -log {compoundOutputFileLuid1} \ -qcResult {compoundOutputFileLuid2}" ``` {% endcode %}

Set Next Step and Copy Concentration

#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------------------ | -------------- | ----------- | ----------------------------------------- | | Criteria 1 - Operator | Text | | Default = >= | | Criteria 1 - Source Data Field | Text | | Default = Concentration | | Criteria 1 - Threshold Value | Numeric | | | | Criteria 2 - Operator | Text | | Default = <= | | Criteria 2 - Source Data Field | Text | | Default = Concentration | | Criteria 1 - Threshold Value | Numeric | | | * Step File Placeholders * Log - Automatically attached * QC Log File - Automatically attached * QC Result File - Automatically attached * Upload File - Manually uploaded * 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 | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Measurement | Concentration | Numeric | | Decimal Places Displayed = 2 | | Measurement | Conc. Units | Text | | | | Project | Project Name | Built-in | | | ### Step 8: Pool Pre-Enriched Libraries - Mass (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Master Step Name = Pool Pre-Enriched Libraries - Mass (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Step Type = Pooling * Aliquot Generation = Fixed, 1 * Naming Convention = {PoolName} #### Automations

Copy Concentration

Calculate Pre-Enriched Library Volume & RSB Volume

* Trigger Location = Record Details * Trigger Style = Manual button {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}

Set Next Step - Advance

Presets

1-plex
12-plex

| | Pre-Enriched Library Sample (ng) | Numeric | Read Only | Default = 500 | | Total Pooled Volume (uL) | Numeric | Read Only | Default = 30 | * Sample Table * Sample Display Default = Expand * Well Sort Order = Row * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------------------------- | -------------- | -------------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Concentration | Numeric | Required Field | Decimal Places Displayed = 2 | | Derived Sample | Conc. Units | Text | Required Field | | | Derived Sample | Pre-Enriched Library Volume (uL) | Numeric | | | | Derived Sample | RSB Volume (uL) | Numeric | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 9: Hybridize Probes (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Master Step Name = Hybridize Probes (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * Illumina DNA Fast Hyb - Enrichment Beads + Buffers * Supplier = Illumina * Catalog Number = 20025519; 20025520 * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/targeted-enrichment/www.illumina.com) * Illumina DNA Fast Hyb - Enrichment PCR + Buffers * Supplier = Illumina * Catalog Number = 20025519; 20025520 * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/targeted-enrichment/www.illumina.com) #### Automations

Set Next Step - Advance

#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ---------------------- | -------------- | ----------- | ----------------------------------------- | | PCR Cycles | Numeric | | | | Thermal Cycler Program | Text | | Default = NF-HYB program | * Step File Placeholders * Log - Automatically attached * Sample Table * Sample Display Default = Expand * Well Sort Order = Row * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 10: Capture Hybridize Probes (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Master Step Name = Capture Hybridize Probes (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * Illumina DNA Fast Hyb - Enrichment Beads + Buffers * Supplier = Illumina * Catalog Number = 20025519; 20025520 * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/targeted-enrichment/www.illumina.com) * Illumina DNA Fast Hyb - Enrichment PCR + Buffers * Supplier = Illumina * Catalog Number = 20025519; 20025520 * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/targeted-enrichment/www.illumina.com) #### Automations

Calculate Total Samples and Calculate Master Mix

Set Next Step - Advance

#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | -------------- | ----------- | ----------------------------------------- | | EE1 (uL) | Numeric | | Decimal Places Displayed = 2 | | HP3 (uL) | Numeric | | Decimal Places Displayed = 2 | | Total Samples | Numeric | | Default = 0 | * Step File Placeholders * Log - Automatically attached * Sample Table * Sample Display Default = Expand * Well Sort Order = Row * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 11: Amplify Enriched Library (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Master Step Name = Amplify Enriched Library (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * Illumina DNA Fast Hyb - Enrichment PCR + Buffers * Supplier = Illumina * Catalog Number = 20025519; 20025520 * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/targeted-enrichment/www.illumina.com) #### Automations

Set Next Step - Advance

#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ---------------------- | -------------- | ----------- | ----------------------------------------- | | PCR Cycles | Numeric | | | | Thermal Cycler Program | Text | | Default = AMP | * Step File Placeholders * Log - Automatically attached * Sample Table * Sample Display Default = Expand * Well Sort Order = Row * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 12: Clean Up Amplified Enriched Library (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Master Step Name = Clean Up Amplified Enriched Library (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * Agencourt AMPure XP Beads * Supplier = Thermo * Catalog Number = NC9959336; NC9933872 * Illumina DNA Prep -Tagmentation (S) Beads * Supplier = Illumina * Catalog Number = 20025519; 20025520 * Website = [illumina.com](https://github.com/illumina-swi/clarity-int-docs/blob/main/docs/int/ipp/other/illumina.com) #### Automations

Set Next Step - Advance

#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### Record Details * Step File Placeholders * Log - Automatically attached * Sample Table * Sample Display Default = Expand * Well Sort Order = Row * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://help.connected.illumina.com/clarity-lims/library-prep/targeted-enrichment/dna-prep-enrich-s-tag-v1.2.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.