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Illumina COVIDSeq v1.6

PreviousReal-Time RT-PCR Prep v1.1 NextRespiratory Virus Panel v1.0

Last updated 2 months ago

Overview

The Illumina COVIDSeq Workflow workflow includes the following functionality:

Preset Illumina COVIDSeq Workflow protocols that track samples through the quantitative detection of SARS-CoV-2 RNA from nasopharyngeal (NP), oropharyngeal (OP), and nasal swab as well as mid-turbinate specimens collected from individuals who meet COVID-19 clinical or epidemiological criteria.
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.
Sample preparation for use on the NovaSeq 6000 Sequencing System.
Parsing of analysis results into Clarity LIMS.

Protocol 1: RNA Extraction (Illumina COVIDSeq Workflow v1.6)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Prep Sample (Illumina COVIDSeq Workflow v1.6)

Master Step Name = Prep Sample (Illumina COVIDSeq Workflow v1.6)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina COVIDSeq Positive Control HT
  - Supplier = Illumina
  - Website = www.illumina.com
- Illumina COVIDSeqTest Box 4
  - Supplier = Illumina
  - Catalog Number = 20043436
  - Website = www.illumina.com

Automations

Set Next Step - Advance

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 = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

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 = For each sample, add 140 µl patient sample, dilution 3 CPC HT, or ELB HT (no template control) to a new 1.7 ml microcentrifuge tube.
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Collapse
- 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
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 2: Purification of RNA - Spin (Illumina COVIDSeq Workflow v1.6)

Master Step Name = Spin Purification of RNA (Illumina COVIDSeq Workflow v1.6)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- QIAmp Viral RNA Mini kit
  - Supplier = Qiagen
  - Catalog Number = (50) - 52904; (250) - 52906
  - Website = https://www.qiagen.com

Automations

Calculate Total Samples

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 \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0}"

Calculate AW1, AW2, AVL Reagent Volumes

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 false -h false \
-exp 'if (step.::No. of Preps:: == 50) {step.::AW1 Concentrate (mL):: = 19 ; step.::EtOH for AW1 (mL):: = 25 ; step.::AW2 Concentrate (mL):: = 13 ; step.::EtOH for AW2 (mL):: = 30} else {step.::AW1 Concentrate (mL):: = 98 ; step.::EtOH for AW1 (mL):: = 130 ; step.::AW2 Concentrate (mL):: = 66 ; step.::EtOH for AW2 (mL):: = 160} ; \
step.::Buffer AVL (mL):: = 0.56 * step.::Total Samples:: ; step.::Carrier RNA-Buffer AVE (uL):: = 10 * step.::Buffer AVL (mL):: ' \
-log {compoundOutputFileLuid0}"

Set Next Step - Advance

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 = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

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
% EtOH
Numeric
Default = 96
Range = 96 To 100
% EtOH Prep Date
Date
AW1 Concentrate (mL)
Numeric
AW2 Concentrate (mL)
Numeric
Buffer AVL (mL)
Numeric
Decimal Places Displayed = 0
Carrier RNA-Buffer AVE (uL)
Numeric
Decimal Places Displayed = 0
Elution Incubation End Time
Numeric
Elution Incubation Start Time
Numeric
EtOH for AW1 (mL)
Numeric
EtOH for AW2 (mL)
Numeric
Instruction Notes
Multiline Text
Read Only
Default = Enter in No. of Preps before clicking on "Calculate AW1, AW2, AVL Reagent Volumes". Elute in 30 µl Buffer AVE instead of 60 µl. Incubate elution for at least 1 minute.
No. of Preps
Numeric Dropdown
Required Field
Custom Entries
Presets
250
50
Default = 250
Total Samples
Numeric
Default = 0
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in