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MiniSeq v1.0

PreviousiSeq 100 Run Setup v1.0 NextMiSeq

Last updated 16 days ago

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)