Illumina DNA PCR-Free Library Prep Manual v1.1

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Last updated 1 month ago

Overview

The Illumina DNA PCR-Free Library Prep Manual workflow includes the following functionality.

Preset Illumina DNA PCR-Free Library Prep Manual protocols that support the preparation of up to 96 dual-indexed paired-end single-stranded libraries from DNA using the Illumina DNA PCR-Free Library Prep 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.

Protocol 1: Sample Prep (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Sort Sample (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Sort Sample (Illumina DNA PCR-Free Library Prep Manual v1.0.3)
Step Type = No Outputs

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

Automations

Set Next Step - DNA PCR-Free Lib Prep

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.::Sample Type for DNA PCR-Free Lib Prep:: == ::gDNA:: && input.::Protocol Type:: == ::Thermal Cycler::) {nextStep = ::Qubit - Thermal Cycler (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::} ; \
if (input.::Sample Type for DNA PCR-Free Lib Prep:: == ::gDNA:: && input.::Protocol Type:: == ::Hybex::) {nextStep = ::Qubit - Hybex (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::} ; \
if (input.::Sample Type for DNA PCR-Free Lib Prep:: == ::Whole Blood:: && input.::Protocol Type:: == ::Thermal Cycler::) {nextStep = ::Whole Blood Lysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::} ; \
if (input.::Sample Type for DNA PCR-Free Lib Prep:: == ::Dried Blood Spot:: && input.::Protocol Type:: == ::Thermal Cycler::) {nextStep = ::Dried Blood Spot Lysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::} ; \
if (input.::Sample Type for DNA PCR-Free Lib Prep:: == ::Saliva:: && input.::Protocol Type::  == ::Thermal Cycler::) {nextStep = ::Saliva Lysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::}' \
-log {compoundOutputFileLuid0}"

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column

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
Instruction Notes
Multiline Text
Read Only
Default = Select a sample type and protocol type for each sample.
Step File Placeholders
- Log - Automatically attached

Sample Table

Sample Display Default = Expand
Well Sort Order = Column

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

Protocol Type

Text Dropdown

Required Field

Presets
- Thermal Cycler
- Hybex
Default = Thermal Cycler

Derived Sample

Sample Name

Built-in

Derived Sample

Sample Type for DNA PCR-Free Lib Prep

Text Dropdown

Required Field

Presets
- gDNA
- Whole Blood
- Dried Blood Spot
- Saliva
Default = gDNA

Project

Project Name

Built-in

Step 2: Qubit - Hybex (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Qubit - Hybex (Illumina DNA PCR-Free Library Prep Manual v1.0.3)
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}

ℹ️ The version of Qubit - Hybex master step name may be different depending on the version of IPP installed.

Automations

Copy Sample Type for DNA PCR-Free Lib Prep

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.::Sample Type:: = input.::Sample Type for DNA PCR-Free Lib Prep:: ' \
-log {compoundOutputFileLuid0}"

Assign QC flags

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 -u {username} -p {password} \
      script:assignQC \
        -i {processURI:v2} \
        -log {compoundOutputFileLuid1} \
        -qcResult {compoundOutputFileLuid2}"

Set Next Step-REMOVE and Copy Concentration & Sample Type

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

Routing - gDNA Hybex

Trigger Location = Step
Trigger Style = Automatic upon exit

bash -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 'Sample Type' \
--FIELD_VALUE 'gDNA' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'Tagment Genomic DNA (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'INPUTS'"

ℹ️ The actual version of the workflow and step names 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 = Column

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

Default = 300
Range = 300 To 2000

Criteria 2 - Operator

Text

Default = <=

Criteria 2 - Source Data Field

Text

Default = Concentration

Criteria 2 - Threshold Value

Numeric

Default = 2000
Range = 300 To 2000

Instruction Notes

Multiline Text

Read Only

Default = 1. Upload or enter Concentration and Conc. Units. 2. Set Threshold Values then click on Assign QC Flags.

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 = Column
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

Derived Sample

Sample Type

Text Dropdown

Required Field
Custom Entries

Presets

Measurement

Concentration

Numeric

Decimal Places Displayed = 2

Measurement

Conc. Units

Text

Measurement

Sample Type

Text

Project

Project Name

Built-in

Step 3: Qubit - Thermal Cycler (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Master Step Name = Qubit - Thermal Cycler (Illumina DNA PCR-Free Library Prep Manual v1.0.3)
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}

ℹ️ The version of Qubit - Thermal Cycler master step name may be different depending on the version of IPP installed.

Automations

Copy Sample Type for DNA PCR-Free Lib Prep

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.::Sample Type:: = input.::Sample Type for DNA PCR-Free Lib Prep:: ' \
-log {compoundOutputFileLuid0}"

Assign QC flags

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 -u {username} -p {password} \
      script:assignQC \
        -i {processURI:v2} \
        -log {compoundOutputFileLuid1} \
        -qcResult {compoundOutputFileLuid2}"

Set Next Step-REMOVE, Set Prep Input Type, Copy Concentration & Sample Type

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 -exp 'nextStep = ::REMOVE:: ; \
if (output.::Concentration:: >= 25 && output.::Concentration:: <= 99) {output.::Prep Input Type:: = ::Low::} ; \
if (output.::Concentration:: >= 100 && output.::Concentration:: <= 2000) {output.::Prep Input Type:: = ::Standard::} ; \
input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units:: ; input.::Sample Type:: = output.::Sample Type::' -log {compoundOutputFileLuid0}"

Routing - gDNA Thermal Cycler

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 Input Type' \
--FIELD_VALUE 'Low' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'Tagment Genomic DNA - Low Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Prep Input Type' \
--FIELD_VALUE 'Standard' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'Tagment Genomic DNA - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'INPUTS'"

ℹ️ The actual version of the workflow and step names 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 = Column

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