Illumina Knowledge Illumina Support Sign In

Illumina DNA Prep with Enrichment (S) Tagmentation v1.2

PreviousTargeted Enrichment NextIllumina RNA Prep with Enrichment (L) Tagmentation v1.1

Last updated 17 days ago

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

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}"

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
  NFE Sample Type
  Text Dropdown
  Required Field
  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
- Flex Lysis Reagent Kit
  - Supplier = Illumina
  - Catalog Number = 20015884
  - Website = www.illumina.com

Automations

Calculate Total Samples & Master Mix

Trigger Location = Record Details
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/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

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Route NFE - Blood

Trigger Location = Step
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -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' "

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

Trigger Location = Record Details
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/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

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

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' "

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