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Illumina DNA Prep (M) Tagmentation v1.0

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Last updated 16 days ago

Overview

The Illumina DNA Prep (M) Tagmentation workflow includes the following functionality.

Preset Illumina DNA Prep (M) Tagmentation protocols that support the generation of enriched libraries for dual-indexed, paired-end sequencing.
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.

Protocol 1: Prep Sample (Illumina DNA Prep (M) Tagmentation v1.0.9)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Sort Sample Type (Illumina DNA Prep (M) Tagmentation v1.0.9)

Master Step Name = Sort Sample v2.0.8
Step Type = No Outputs

The version of Sort Sample master step name may be different depending on the version of IPP installed.

Automations

Set Next Step - Tagmentation

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'if (input.::Prep Sample Type - Tagmentation:: == ::Large Complex Genomes::) {nextStep = ::REMOVE::} ; \
if (input.::Prep Sample Type - Tagmentation:: == ::Small Genomes::) {nextStep = ::DNA Quantification (Illumina DNA Prep (M) Tagmentation v1.0.9)::} ; \
if (input.::Prep Sample Type - Tagmentation:: == ::Saliva::) {nextStep = ::Saliva Lysis (Illumina DNA Prep (M) Tagmentation v1.0.9)::} ; \
if (input.::Prep Sample Type - Tagmentation:: == ::Blood::) {nextStep = ::Blood Lysis (Illumina DNA Prep (M) Tagmentation v1.0.9)::} ' -log {compoundOutputFileLuid0}"

ℹ The version of the nextStep step names may be different depending on the version of IPP installed.

Route Samples - Large Complex Genome

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 'Prep Sample Type - Tagmentation' \
--FIELD_VALUE 'Large Complex Genomes' \
--WORKFLOW 'Illumina DNA Prep (M) Tagmentation v1.0.9' \
--STEP 'Tagment Genomic DNA (Illumina DNA Prep (M) Tagmentation v1.0.9)' \
--INPUTS_OR_OUTPUTS 'INPUTS' "

ℹ The actual version of the workflows and steps in the routing automation 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
Comment
Multiline Text
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
  Prep Sample Type - Tagmentation
  Text Dropdown
  Required Field
  Presets
  Blood
  Saliva
  Large Complex Genomes
  Small Genomes
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 2: DNA Quantification (Illumina DNA Prep (M) Tagmentation v1.0.9)

Master Step Name = DNA Quantification (Illumina DNA Prep (M) Tagmentation v1.0.9)
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}

The version of DNA Quantification master step name may be different depending on the version of IPP installed.

Automations

Calculate DNA Amount & Assign QC

Trigger Location = Record Details
Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'output.::DNA Amount (ng):: = output.::Concentration (ng/ul):: * output.::Sample Volume (ul)::' -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 true -h false -exp 'if (output.::DNA Amount (ng):: >= 0.33 && output.::DNA Amount (ng):: <= 100) { output.QC = true } else { output.QC = false } ; input.::DNA Amount (ng):: = output.::DNA Amount (ng):: ; input.::Concentration (ng/ul):: = output.::Concentration (ng/ul):: ; output.::Prep Sample Type - Tagmentation:: = input.::Prep Sample Type - Tagmentation::' -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 Samples - Small Genomes

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 'Prep Sample Type - Tagmentation' \
--FIELD_VALUE 'Small Genomes' \
--WORKFLOW 'Illumina DNA Prep (M) Tagmentation v1.0.9' \
--STEP 'Tagment Genomic DNA (Illumina DNA Prep (M) Tagmentation v1.0.9)' \
--INPUTS_OR_OUTPUTS 'INPUTS' "

ℹ The actual version of the workflows and steps in the routing automation 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
Comment
Multiline Text
Step File Placeholders
- Log - 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
  Prep Sample Type - Tagmentation
  Text Dropdown
  Required Field
  Presets
  Blood
  Saliva
  Large Complex Genomes
  Small Genomes
  Derived Sample
  Sample Name
  Built-in
  Measurement
  Concentration (ng/ul)
  Numeric
  Decimal Places Displayed = 2
  Measurement
  DNA Amount (ng)
  Numeric
  Decimal Places Displayed = 0
  Measurement
  Prep Sample Type - Tagmentation
  Text
  Read Only
  Measurement
  Sample Volume (ul)
  Numeric
  Required Field
  Decimal Places Displayed = 2
  Project
  Project Name
  Built-in

Step 3: Blood Lysis (Illumina DNA Prep (M) Tagmentation v1.0.9)

Master Step Name = Blood Lysis (Illumina DNA Prep (M) Tagmentation v1.0.9)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Box 1
  - Supplier = Illumina
- Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Flex Lysis Reagent Kit
  - Supplier = Illumina

The version of Blood Lysis master step name may be different depending on the version of IPP installed.

Automations

Count Samples and Calculate 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.::Prep Sample Type - Tagmentation:: = input.::Prep Sample Type - Tagmentation:: ; \
step.::BLB (uL):: = step.::Total Samples:: * 7 ; \
step.::PK1 (uL):: = step.::Total Samples:: * 2 ; \
step.::Nuclease-free water (uL):: = step.::Total Samples:: * 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 Samples - 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 'Prep Sample Type - Tagmentation' \
--FIELD_VALUE 'Blood' \
--WORKFLOW 'Illumina DNA Prep (M) Tagmentation v1.0.9' \
--STEP 'Tagment Genomic DNA (Illumina DNA Prep (M) Tagmentation v1.0.9)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' "

ℹ The actual version of the workflows and steps in the routing automation 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% Ethanol Prep Date
Date
BLB (uL)
Numeric
Decimal Places Displayed = 2
Comment
Multiline Text
Nuclease-free water (uL)
Numeric
Decimal Places Displayed = 2
PK1 (uL)
Numeric
Decimal Places Displayed = 2
Thermal Cycler Program
Text
Default = BLP
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