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Respiratory Virus Panel v1.0

PreviousIllumina COVIDSeq v1.6 NextCompatibility

Last updated 17 days ago

Overview

The Respiratory Virus Panel workflow includes the following functionality:

Preconfigured protocols that support the preparation of upper and lower respiratory specimens for real-time RT-PCR qualitative detection of nucleic acid from the 2019-nCoV.
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.
Routing to iSeq, MiniSeq, MiSeq, NextSeq 550, NextSeq 2000.

Protocol 1: Sort Sample Type (Respiratory Virus Panel v1.0)

Protocol Type = Other

Next Steps Configuration

Step 1: Sort Sample Type (Respiratory Virus Panel v1.0)

Master Step Name = Sort Sample Type (Respiratory Virus Panel v1.0)
Step Type = No Outputs

Automations

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}"

Routing Script - Extraction

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 {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Respiratory Virus Extraction Protocol' \
--FIELD_VALUE 'QIAamp Viral Mini Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'Sample Concentration (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Respiratory Virus Extraction Protocol' \
--FIELD_VALUE 'AllPrep PowerViral DNA/RNA Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'Sort Sample (Respiratory Virus Panel v1.0)' \
--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
Instruction
Multiline Text
Read Only
Default = Please select the Respiratory Virus Extraction Protocol for each sample.
Step File Placeholders
- Log File - 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
  Respiratory Virus Extraction Protocol
  Text Dropdown
  Required Field
  Presets
  QIAamp Viral Mini Kit
  AllPrep PowerViral DNA/RNA Kit
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Protocol 2: QIAamp Viral RNA Mini Kit (Respiratory Virus Panel v1.0)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Sample Concentration (Respiratory Virus Panel v1.0)

Master Step Name = Sample Concentration (Respiratory Virus Panel v1.0)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}

Automations

Set Next Step - Purification

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.::Is Bead Beating Required?:: == ::Yes::) {nextStep = ::Prep Samples - Bead Beating (Respiratory Virus Panel v1.0)::} \
else {if (input.::Is Bead Beating Required?:: == ::No::) {nextStep = ::Prep Samples (Respiratory Virus Panel v1.0)::} }' \
-log {compoundOutputFileLuid0}"

ℹ The actual version of the Prep Samples - Bead Beating and Prep Samples steps 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
Sample Volume (mL)
Numeric
Default = 3.5
Directions
Multiline Text
Default = Add up to 3.5 ml of sample to the microconcentrator Centrifuge to a final volume of 140 μl.
Step File Placeholders
- Log File - 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
  Derived Sample
  Purification Protocol
  Text Dropdown
  Required Field
  Presets
  Spin
  Vacuum
  Derived Sample
  Sample Name
  Built-in

Step 2: Purification of Viral RNA - Spin Protocol (Respiratory Virus Panel v1.0)

Master Step Name = Purification of Viral RNA - Spin Protocol (Respiratory Virus Panel v1.0)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Buffer AW1
  - Catalog Number = 61904
- Buffer AW2
  - Catalog Number = 61904

Automations

Calculate Total Samples and 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 'step.::Buffer AVL Volume (ml):: = step.::Total Samples:: * 0.56 ; \
step.::Carrier RNA AVE Volume (uL):: = step.::Buffer AVL Volume (ml):: * 10 ' \
-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}"

Routing Script - cDNA synthesis

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 {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'Maxima H Minus Double-Stranded cDNA Synthesis Kit' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'First Strand cDNA Synthesis (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'NEBNext Ultra II First Strand Synthesis Module' \
--WORKFLOW 'Respiratory Virus Panel v1.0' \
--STEP 'mRNA Isolation, Fragmentation and Priming (Respiratory Virus Panel v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'cDNA Synthesis Protocol' \
--FIELD_VALUE 'SuperScript Double-Stranded cDNA Synthesis Kit' \