MiniSeq v1.0

Overview

The MiniSeq workflow includes the following functionality.

Preconfigured protocols that support the preparation of small genome, amplicon, targeted enrichment, and RNA sequencing using low library volumes for 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: Select Normalization Variation (MiniSeq v1.0)

Protocol Type = Sequencing

Next Steps Configuration

Step 1: Select Normalization Variation (MiniSeq v1.0)

Master Step Name = Select Normalization Variation (MiniSeq 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 for Normalization Variation

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 'Normalization Variation' \
--FIELD_VALUE 'Standard Normalization' \
--WORKFLOW 'MiniSeq v1.0' \
--STEP 'Create Normalized Library Pool (MiniSeq v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Normalization Variation' \
--FIELD_VALUE 'Bead-Based Normalization' \
--WORKFLOW 'MiniSeq v1.0' \
--STEP 'Dilute Library Pool to Loading Concentration and Denature - Bead Based (MiniSeq v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Normalization Variation' \
--FIELD_VALUE 'AmpliSeq for Illumina Normalization' \
--WORKFLOW 'MiniSeq v1.0' \
--STEP 'Dilute Libraries - AmpliSeq (MiniSeq v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Normalization Variation' \
--FIELD_VALUE 'AmpliSeq Library Equalizer for Illumina Normalization' \
--WORKFLOW 'MiniSeq v1.0' \
--STEP 'Pool Libraries - AmpliSeq Equalizer (MiniSeq v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS' "

ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.

Set Next Step - Advance

Trigger Location = Not Used

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
Comment
Multiline Text
Instruction Notes
Multiline Text
Read Only
Default = Select a Normalization Variation protocol 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
  Sample Name
  Built-in
  Derived Sample
  Normalization Variation
  Text Dropdown
  Required Field
  Presets
  Standard Normalization
  Bead-Based Normalization
  AmpliSeq for Illumina Normalization
  AmpliSeq Library Equalizer for Illumina Normalization
  Default = Standard Normalization
  Project
  Project Name
  Built-in

Protocol 2: Standard Normalization (MiniSeq v1.0)

Protocol Type = Sequencing

Next Steps Configuration

Step 1: Create Normalized Library Pool (MiniSeq v1.0)

Master Step Name = Create Normalized Library Pool (MiniSeq v1.0)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Resuspension Buffer (RSB)

Automations

Calculate Library & RSB Volumes - MiniSeq

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:http} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false \
-exp 'output.::Library (uL):: = (step.::Final Molarity (nM):: * step.::Final Volume (uL)::) / output.::Library Molarity (nM):: ; \
output.::RSB (uL):: = step.::Final Volume (uL):: - output.::Library (uL):: ; 
output.::Final Molarity (nM):: = step.::Final Molarity (nM)::' \
-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
Final Molarity (nM)
Numeric
Default = 10
Range = 1 To 10
Decimal Places Displayed = 0
Final Volume (uL)
Numeric
Default = 10
Range = 10 To 400
Decimal Places Displayed = 0
Instruction Notes
Multiline Text
Read Only
Default = - Enter in Final Molarity (nM), Final Volume (uL) and Library Molarity (nM) before clicking on calculation button. - Add 10 uL of each 10 nM library to a new microcentrifuge tube.
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
  Final Molarity (nM)
  Numeric
  Derived Sample
  Library Molarity (nM)
  Numeric
  Required Field
  Derived Sample
  Library (uL)
  Numeric
  Decimal Places Displayed = 0
  Derived Sample
  RSB (uL)
  Numeric
  Decimal Places Displayed = 0
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 2: Dilute Library Pool (MiniSeq v1.0)

Master Step Name = Dilute Library Pool (MiniSeq v1.0)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Resuspension Buffer (RSB)

Automations

Copy Library Pool Molarity

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:http} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false \
-exp 'output.::Library Pool (nM):: = input.::Final Molarity (nM)::' \
-log {compoundOutputFileLuid0}"

Calculate Library Pool & RSB Volumes - MiniSeq

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:http} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false \
-exp 'output.::Library Pool (uL):: = (step.::Final Molarity (nM):: * step.::Final Volume (uL)::) / output.::Library Pool (nM):: ; \
output.::RSB (uL):: = step.::Final Volume (uL):: - output.::Library Pool (uL)::' \
-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
Final Molarity (nM)
Numeric
Default = 1
Final Volume (uL)
Numeric
Default = 100
Instruction Notes
Multiline Text
Read Only
Default = Enter in Final Molarity (nM), and Final Volume (uL) before clicking on calculation button.
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
  Library Pool (nM)
  Numeric
  Decimal Places Displayed = 0
  Derived Sample
  Library Pool (uL)
  Numeric
  Decimal Places Displayed = 0
  Derived Sample
  RSB (uL)
  Numeric
  Decimal Places Displayed = 0
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 3: Denature Library Pool (MiniSeq v1.0)

Master Step Name = Denature Library Pool (MiniSeq v1.0)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- 0.1 N NaOH
- 200 mM Tris-HCl, pH 7.0

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 = - Combine 5 uL of 1 nM Library Pool and 5 uL of 0.1 N NaOH in a microcentridge tube. - Vortex briefly and then centrifuge at 280 × g for 1 minute. - Incubate at room temperature for 5 minutes. - Add 5 µl 200 mM Tris-HCl, pH 7.0. Vortex briefly and then centrifuge at 280 × g for 1 minute.
Step File Placeholders
- Log - 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 4: Dilute to Loading Concentration (MiniSeq v1.0)

Master Step Name = Dilute to Loading Concentration (MiniSeq v1.0)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Hybridization Buffer
  - Supplier = Illumina; part of MiniSeq High Output Reagent Kit
  - Catalog Number = 75 cycles - FC-420-1001; 150 cycles - FC-420-1002; 300 cycles - FC-420-1003
  - 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}"

Routing Script for MiniSeq

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 'Add PhiX Control' \
--FIELD_VALUE 'No' \
--WORKFLOW 'MiniSeq v1.0' \
--STEP 'Run Setup (MiniSeq v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Add PhiX Control' \
--FIELD_VALUE 'Yes' \
--WORKFLOW 'MiniSeq v1.0' \
--STEP 'Dilute Stock PhiX (MiniSeq v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.

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
Add PhiX Control
Text Dropdown
Required Field
Presets
No
Yes
Default = No
Instruction Notes
Multiline Text
Read Only
Default = - Add 985 µl of prechilled Hybridization Buffer to the tube of denatured library. - The total volume is 1 ml at 5 pM. - Vortex briefly and then centrifuge at 280 × g for 1 minute. - Transfer 180 µl diluted library to a new microcentrifuge tube. - Add 320 µl prechilled Hybridization Buffer. - The total volume is 500 µl at 1.8 pM.
Loading Concentration (pM)
Numeric
Default = 1.8
Total Volume (uL)
Numeric
Default = 500
Step File Placeholders
- Log - 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

Protocol 3: Bead-Based Normalization (MiniSeq v1.0)

Protocol Type = Sequencing

Next Steps Configuration

Step 1: Dilute Library Pool to Loading Concentration and Denature - Bead Based (MiniSeq v1.0)

Master Step Name = Dilute Library Pool to Loading Concentration and Denature - Bead Based (MiniSeq v1.0)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Hybridization Buffer
  - Supplier = Illumina; part of MiniSeq High Output Reagent Kit
  - Catalog Number = 75 cycles - FC-420-1001; 150 cycles - FC-420-1002; 300 cycles - FC-420-1003
  - Website = www.illumina.com

Automations

Calculate Prechilled Hybridization Buffer Volumes - MiniSeq

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:http} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false \
-exp 'output.::Prechilled Hybridization Buffer (uL):: = output.::Final Volume (uL):: - output.::Library Pool (uL)::' \
-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}"

Routing Script for MiniSeq

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 'Add PhiX Control' \
--FIELD_VALUE 'No' \
--WORKFLOW 'MiniSeq v1.0' \
--STEP 'Run Setup (MiniSeq v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Add PhiX Control' \
--FIELD_VALUE 'Yes' \
--WORKFLOW 'MiniSeq v1.0' \
--STEP 'Dilute Stock PhiX (MiniSeq v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.

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
Add PhiX Control
Text Dropdown
Required Field
Presets
No
Yes
Default = No
Instruction Notes
Multiline Text
Read Only
Default = - Enter in Library Pool and Final Volume before clicking on calculation button. - Vortex briefly and then centrifuge at 280 × g for 1 minute. - Transfer 250 µl diluted library to a new microcentrifuge tube. - Add 250 µl prechilled Hybridization Buffer. - Vortex briefly and then centrifuge at 280 × g for 1 minute. - To denture the diluted library pool, place the tube in the incubator for 2 minutes. Immediately cool on ice and leave it on ice for 5 minutes.
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
  Final Volume (uL)
  Numeric
  Decimal Places Displayed = 0
  Derived Sample
  Library Pool (uL)
  Numeric
  Decimal Places Displayed = 0
  Derived Sample
  Prechilled Hybridization Buffer (uL)
  Numeric
  Decimal Places Displayed = 0
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Protocol 4: AmpliSeq for Illumina Normalization (MiniSeq v1.0)

Protocol Type = Sequencing

Next Steps Configuration

Step 1: Dilute Libraries - AmpliSeq (MiniSeq v1.0)

Master Step Name = Dilute Libraries - AmpliSeq (MiniSeq v1.0)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Low TE
  - Supplier = Supplier - Illumina; part of AmpliSeq Library Plus Kit
  - Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
  - Website = www.illumina.com

Automations

Copy Final Molarity

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.::Final Molarity (nM):: = step.::Final Molarity (nM)::' \
-log {compoundOutputFileLuid0}"

Calculate Starting Molarity and Library & Low TE Volumes - MiniSeq

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:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false \
-exp 'output.::Starting Molarity (nM):: = (output.::Concentration:: * 1000000) / (660 * output.::Average Library Size (bp)::) ; \
output.::Library (uL):: = (output.::Final Molarity (nM):: * step.::Final Volume (uL)::) / output.::Starting Molarity (nM):: ; \
output.::Low TE (uL):: = step.::Final Volume (uL):: - output.::Library (uL)::' \
-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
Final Molarity (nM)
Numeric
Default = 2
Final Volume (uL)
Numeric
Default = 50
Instruction Notes
Multiline Text
Read Only
Default = Enter in the concentration and average library size before clicking on the calculation button.
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
  Average Library Size (bp)
  Numeric
  Default = 350
  Derived Sample
  Concentration
  Numeric
  Required Field
  Decimal Places Displayed = 2
  Derived Sample
  Conc. Units
  Text
  Required Field
  Derived Sample
  Final Molarity (nM)
  Numeric
  Derived Sample
  Library (uL)
  Numeric
  Decimal Places Displayed = 0
  Derived Sample
  Low TE (uL)
  Numeric
  Decimal Places Displayed = 2
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Starting Molarity (nM)
  Numeric
  Decimal Places Displayed = 0
  Project
  Project Name
  Built-in

Step 2: Pool Libraries - AmpliSeq (MiniSeq v1.0)

Master Step Name = Pool Libraries - AmpliSeq (MiniSeq v1.0)
Step Type = Pooling
Aliquot Generation = Fixed, 1
Naming Convention = {PoolName}
Reagent Kits
- Low TE
  - Supplier = Supplier - Illumina; part of AmpliSeq Library Plus Kit
  - Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
  - Website = www.illumina.com

Automations

Copy Molarity - MiniSeq

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.::Molarity (nM):: = input.::Final Molarity (nM)::' \
-log {compoundOutputFileLuid0}"

Calculate DNA to RNA - MiniSeq

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.::AmpliSeq for Illumina Panel:: == ::Myeloid Panel::) {step.::DNA to RNA Ratio:: = ::8:1::} ; \
if (step.::AmpliSeq for Illumina Panel:: == ::Childhood Cancer Panel::) {step.::DNA to RNA Ratio:: = ::5:1::} ; \
if (step.::AmpliSeq for Illumina Panel:: == ::Focus Panel::) {step.::DNA to RNA Ratio:: = ::7:3::} ; \
if (step.::AmpliSeq for Illumina Panel:: == ::Comprehensive Panel v3::) {step.::DNA to RNA Ratio:: = ::25:1::}' \
-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

Pooling

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

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
AmpliSeq for Illumina Panel
Text Dropdown
Required Field
Presets
Childhood Cancer Panel
Comprehensive Panel
Focus Panel
Myeloid Panel
Default = Childhood Cancer Panel
DNA to RNA Ratio
Text
Instruction Notes
Multiline Text
Read Only
Default = - Select the AmpliSeq for Illumina Panel before clicking on Calculate DNA to RNA ratio button. - Combine equal library volumes to a 1.5 mL LoBind tube. - User different tubes for DNA and RNA Libraries. - Combine DNA to RNA ratio in a new tube.
Transfer Library Volume (uL)
Numeric
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
  Molarity (nM)
  Numeric
  Decimal Places Displayed = 2
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 3: Denature Libraries - AmpliSeq (MiniSeq v1.0)

Master Step Name = Denature Libraries - AmpliSeq (MiniSeq v1.0)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Low TE
  - Supplier = Supplier - Illumina; part of AmpliSeq Library Plus Kit
  - Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
  - Website = www.illumina.com

Automations

Copy Molarity - MiniSeq

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.::Molarity (nM):: = input.::Molarity (nM)::' \
-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
0.2 N NaOH
Numeric
Default = 10
0.2 N NaOH Prep Date
Date
200 mM Tris-HCl, pH 7.0
Numeric
Default = 10
Instruction Notes
Multiline Text
Read Only
Default = - Combine Pool Libraries and 0.2 N NaOH volumes. - Vortex briefly. Incubate at room temp for 5 mins. - Add 10 µl 200 mM Tris-HCl, pH 7.0 to the tube. Vortex briefly.
Pool Libraries (uL)
Numeric
Default = 10
Step File Placeholders
- Log - 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
  Molarity (nM)
  Numeric
  Decimal Places Displayed = 2
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 4: Dilute Denatured Libraries to Loading Concentration - AmpliSeq (MiniSeq v1.0)

Master Step Name = Dilute Denatured Libraries to Loading Concentration - AmpliSeq (MiniSeq v1.0)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- HT1
  - Supplier = Illumina; part of AmpliSeq Library Plus Kit
  - Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103 Website - www.illumina.com
  - Website = www.illumina.com

Automations

Calculate Diluted Denatured Libraries & Prechilled HT1 Volumes - MiniSeq

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 'output.::Diluted Denatured Libraries (uL):: = (step.::Loading Concentration (pM):: * step.::Final Volume (uL)::) / output.::Diluted Denatured Libraries (pM):: ; \
output.::Prechilled HT1(uL):: = step.::Final Volume (uL):: - output.::Diluted Denatured Libraries (uL)::' \
-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}"

Routing Script for MiniSeq

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 'Add PhiX Control' \
--FIELD_VALUE 'No' \
--WORKFLOW 'MiniSeq v1.0' \
--STEP 'Run Setup (MiniSeq v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Add PhiX Control' \
--FIELD_VALUE 'Yes' \
--WORKFLOW 'MiniSeq v1.0' \
--STEP 'Dilute Stock PhiX (MiniSeq v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.

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
200 mM Tris-HCl, pH 7.0
Numeric
Default = 10
Add PhiX Control
Text Dropdown
Custom Entries
Presets
No
Yes
Default = No
Final Volume (uL)
Numeric
Default = 1000
Instruction Notes
Multiline Text
Read Only
Default = - Enter Loading Concentration before clicking on the calculation button. - Add 970 uL of prechilled HT1 to denatured library pool. - Dilute to loading concentration by combining Diluted Denatured Libraries and Prechilled HT1 volumes.
Loading Concentration (pM)
Numeric
Default = 1.8
Range = 1.1 To 1.9
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
  Diluted Denatured Libraries (pM)
  Numeric
  Default = 20
  Derived Sample
  Diluted Denatured Libraries (uL)
  Numeric
  Decimal Places Displayed = 0
  Derived Sample
  Prechilled HT1(uL)
  Numeric
  Decimal Places Displayed = 0
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Protocol 5: AmpliSeq Library Equalizer for Illumina Normalization (MiniSeq v1.0)

Protocol Type = Sequencing

Next Steps Configuration

Step 1: Pool Libraries - AmpliSeq Equalizer (MiniSeq v1.0)

Master Step Name = Pool Libraries - AmpliSeq (MiniSeq v1.0)
Step Type = Pooling
Aliquot Generation = Fixed, 1
Naming Convention = {PoolName}
Reagent Kits
- Low TE
  - Supplier = Supplier - Illumina; part of AmpliSeq Library Plus Kit
  - Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
  - Website = www.illumina.com

Automations

Copy Molarity - MiniSeq

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.::Molarity (nM):: = input.::Final Molarity (nM)::' \
-log {compoundOutputFileLuid0}"

Calculate DNA to RNA - MiniSeq

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.::AmpliSeq for Illumina Panel:: == ::Myeloid Panel::) {step.::DNA to RNA Ratio:: = ::8:1::} ; \
if (step.::AmpliSeq for Illumina Panel:: == ::Childhood Cancer Panel::) {step.::DNA to RNA Ratio:: = ::5:1::} ; \
if (step.::AmpliSeq for Illumina Panel:: == ::Focus Panel::) {step.::DNA to RNA Ratio:: = ::7:3::} ; \
if (step.::AmpliSeq for Illumina Panel:: == ::Comprehensive Panel v3::) {step.::DNA to RNA Ratio:: = ::25:1::}' \
-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

Pooling

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

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
AmpliSeq for Illumina Panel
Text Dropdown
Required Field
Presets
Childhood Cancer Panel
Comprehensive Panel
Focus Panel
Myeloid Panel
Default = Childhood Cancer Panel
DNA to RNA Ratio
Text
Instruction Notes
Multiline Text
Read Only
Default = - Select the AmpliSeq for Illumina Panel before clicking on Calculate DNA to RNA ratio button. - Combine equal library volumes to a 1.5 mL LoBind tube. - User different tubes for DNA and RNA Libraries. - Combine DNA to RNA ratio in a new tube.
Transfer Library Volume (uL)
Numeric
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
  Molarity (nM)
  Numeric
  Decimal Places Displayed = 2
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 2: Denature Libraries - AmpliSeq Equalizer (MiniSeq v1.0)

Master Step Name = Denature Libraries - AmpliSeq (MiniSeq v1.0)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Low TE
  - Supplier = Supplier - Illumina; part of AmpliSeq Library Plus Kit
  - Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
  - Website = www.illumina.com

Automations

Copy Molarity - MiniSeq

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.::Molarity (nM):: = input.::Molarity (nM)::' \
-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
0.2 N NaOH
Numeric
Default = 10
0.2 N NaOH Prep Date
Date
200 mM Tris-HCl, pH 7.0
Numeric
Default = 10
Instruction Notes
Multiline Text
Read Only
Default = - Combine Pool Libraries and 0.2 N NaOH volumes. - Vortex briefly. Incubate at room temp for 5 mins. - Add 10 µl 200 mM Tris-HCl, pH 7.0 to the tube. Vortex briefly.
Pool Libraries (uL)
Numeric
Default = 10
Step File Placeholders
- Log - 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
  Molarity (nM)
  Numeric
  Decimal Places Displayed = 2
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 3: Dilute Denatured Libraries to Loading Concentration - AmpliSeq Equalizer (MiniSeq v1.0)

Master Step Name = Dilute Denatured Libraries to Loading Concentration - AmpliSeq (MiniSeq v1.0)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- HT1
  - Supplier = Illumina; part of AmpliSeq Library Plus Kit
  - Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103 Website - www.illumina.com
  - Website = www.illumina.com

Automations

Calculate Diluted Denatured Libraries & Prechilled HT1 Volumes - MiniSeq

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 'output.::Diluted Denatured Libraries (uL):: = (step.::Loading Concentration (pM):: * step.::Final Volume (uL)::) / output.::Diluted Denatured Libraries (pM):: ; \
output.::Prechilled HT1(uL):: = step.::Final Volume (uL):: - output.::Diluted Denatured Libraries (uL)::' \
-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}"

Routing Script for MiniSeq

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 'Add PhiX Control' \
--FIELD_VALUE 'No' \
--WORKFLOW 'MiniSeq v1.0' \
--STEP 'Run Setup (MiniSeq v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Add PhiX Control' \
--FIELD_VALUE 'Yes' \
--WORKFLOW 'MiniSeq v1.0' \
--STEP 'Dilute Stock PhiX (MiniSeq v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.

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
200 mM Tris-HCl, pH 7.0
Numeric
Default = 10
Add PhiX Control
Text Dropdown
Custom Entries
Presets
No
Yes
Default = No
Final Volume (uL)
Numeric
Default = 1000
Instruction Notes
Multiline Text
Read Only
Default = - Enter Loading Concentration before clicking on the calculation button. - Add 970 uL of prechilled HT1 to denatured library pool. - Dilute to loading concentration by combining Diluted Denatured Libraries and Prechilled HT1 volumes.
Loading Concentration (pM)
Numeric
Default = 1.8
Range = 1.1 To 1.9
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
  Diluted Denatured Libraries (pM)
  Numeric
  Default = 20
  Derived Sample
  Diluted Denatured Libraries (uL)
  Numeric
  Decimal Places Displayed = 0
  Derived Sample
  Prechilled HT1(uL)
  Numeric
  Decimal Places Displayed = 0
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Protocol 6: Add PhiX Control (MiniSeq v1.0)

Protocol Type = Sequencing

Next Steps Configuration

Step 1: Dilute Stock PhiX (MiniSeq v1.0)

Master Step Name = Dilute Stock PhiX (MiniSeq v1.0)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Resuspension Buffer (RSB)
Control Types
- PhiX v3
  - Supplier = Illumina
  - Catalog Number = FC-110-3001
  - Website = http://www.illumina.com/products/phix_control_v3.ilmn

Automations

Calculate Stock PhiX and RSB 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 'step.::Stock PhiX Volume (uL):: = (step.::Final PhiX Molarity (nM):: * step.::Final PhiX Volume (uL)::) / step.::Stock PhiX Molarity (nM):: ; \
step.::RSB (uL):: = step.::Final PhiX Volume (uL):: - step.::Stock PhiX Volume (uL)::' \
-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
Final PhiX Molarity (nM)
Numeric
Default = 4
Final PhiX Volume (uL)
Numeric
Default = 25
Instruction Notes
Multiline Text
Read Only
Default = Enter Stock PhiX (nM), Final PhiX Molarity (nM), and Final Volume (uL) before clicking on calculation button.
RSB (uL)
Numeric
Decimal Places Displayed = 0
Stock PhiX Molarity (nM)
Numeric
Default = 10
Stock PhiX Volume (uL)
Numeric
Decimal Places Displayed = 0
Step File Placeholders
- Log - 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: Denature PhiX (MiniSeq v1.0)

Master Step Name = Denature PhiX (MiniSeq v1.0)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- 0.1 N NaOH
- 200 mM Tris-HCl, pH 7.0

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 = - Combine 5uL of 4 nM PhiX and 5 uL of 0.1 N NaOH. - Vortex briefly and then pulse centrifuge. - Incubate at room temperature for 5 minutes. - Add 5 µl 200 mM Tris-HCl, pH 7.0. - Vortex briefly and then centrifuge at 280 × g for 1 minute.
Step File Placeholders
- Log - 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 3: Dilute PhiX to Loading Concentration and Combine Library & PhiX (MiniSeq v1.0)

Master Step Name = Dilute PhiX to Loading Concentration and Combine Library & PhiX (MiniSeq v1.0)
Step Type = Pooling
Aliquot Generation = Fixed, 1
Naming Convention = {PoolName}
Reagent Kits
- Hybridization Buffer * Supplier = Illumina; part of MiniSeq High Output Reagent Kit * Catalog Number = 75 cycles - FC-420-1001; 150 cycles - FC-420-1002; 300 cycles - FC-420-1003 * Website = www.illumina.com

Automations

Calculate Denatured PhiX and Prechilled Hybridization Buffer 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 'step.::Denatured PhiX Volume (uL):: = (step.::Final Denatured PhiX Molarity (pM):: * step.::Final Volume (uL)::) / step.::Denatured PhiX Molarity (pM):: ; \
step.::Prechilled Hybridization Buffer (uL):: = step.::Final Volume (uL):: - step.::Denatured PhiX Volume (uL)::' \
-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

Pooling

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

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Denatured PhiX Molarity (pM)
Numeric
Default = 20
Denatured PhiX Volume (uL)
Numeric
Decimal Places Displayed = 0
Final Denatured PhiX Molarity (pM)
Numeric
Default = 1.8
Final Volume (uL)
Numeric
Default = 500
Instruction Notes
Multiline Text
Read Only
Default = - Enter Denatured PhiX Molarity (pM), Final Denatured PhiX Molarity (pM) and Final Volume (uL) before clicking on calculation button. - Add Denatured PhiX and Prechilled Hybridization Buffer volumes too dilute the denatured PhiX. - Invert to mix and then centrifuge at 280 × g for 1 minute. - Combine 5 uL of denatured and diluted PhiX control with 500 uL of denatured and diluted library pool.
Prechilled Hybridization Buffer (uL)
Numeric
Decimal Places Displayed = 0
Step File Placeholders
- Log - 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

Protocol 7: Run Setup (MiniSeq v1.0)

Protocol Type = Sequencing

Next Steps Configuration

Step 1: Run Setup (MiniSeq v1.0)

Master Step Name = Run Setup (MiniSeq v1.0)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- MiniSeq High Output Reagent Kit
  - Supplier = Illumina
  - Catalog Number = 75 cycles - FC-420-1001; 150 cycles - FC-420-1002; 300 cycles - FC-420-1003
  - Website = www.illumina.com

Automations

1. miniseq sample sheet

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/DriverFileGenerator.jar -i {processURI:v2} -u {username} -p {password} \
script:driver_file_generator \
-t /opt/gls/clarity/extensions/conf/driverfiletemplates/miniSeq_Samplesheet.csv \
-o {compoundOutputFileLuid1}.csv \
-q true \
-destLIMSID {compoundOutputFileLuid1} \
-l {compoundOutputFileLuid2}"

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

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Row
Destination Containers
- MiniSeq Reagent Cartridge

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Adapter
Text
Default = CTGTCTCTTATACACATCT
BaseSpace Sequence Hub
Text Dropdown
Custom Entries
Presets
Run Monitoring Only
Run Monitoring and Storage
Chemistry
Text
Custom Primer for Read 1
Text
Customer Primer for Index 1
Text
Customer Primer for Read 2
Text
Customer Primer for Index 2
Text
Experiment Name
Text
Required Field
Index 1 (i7 Primer) Cycles
Text
Required Field
Default = 8
Index 2 (i5 Primer) Cycles
Text
Required Field
Default = 8
Instruction Notes
Multiline Text
Read Only
Default = Add 500 uL of prepared libraries to reagent cartridge.
Local Run Manager Analysis Id
Text
Manifest File Name
Text
Module
Text
Output Folder Location
Text
Read 1 Cycles
Numeric
Required Field
Range = 0 To 151
Read 2 Cycles
Numeric
Required Field
Range = 0 To 151
Read Type
Text Dropdown
Required Field
Presets
Paired End Read
Single Read
Default = Paired End Read
Workflow
Text
Default = GenerateFASTQ
Step File Placeholders
- Log - Automatically attached
- LRM Sample Sheet - Automatically attached
- Manual Sample Sheet - 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

PreviousiSeq 100 Run Setup v1.0 NextMiSeq

Last updated 5 months ago

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