iSeq 100 Run Setup v1.0

Overview

The iSeq 100 Run Setup includes the following functionality.

Preconfigured iSeq 100 Run Setup workflow that supports the preparation of samples for use on the Illumina® iSeq™ 100 Sequencing System provides a targeted approach to next-generation sequencing (NGS).
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.
Local Run Manager and manual sample sheet generation for use on the iSeq 100.

Protocol 1: Dilute Libraries and Run Setup (iSeq 100 v1.0)

Protocol Type = Sequencing

Next Steps Configuration

Step 1: Dilute Library to 1nM (iSeq 100 v1.0)

Master Step Name = Dilute Library to 1nM - iSeq 100 v1.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Resuspension Buffer (RSB)

Automations

Calculate Final & Library Volumes - iSeq

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 'if (step.::Library Prep Kit:: == ::100% PhiX::) {step.::Final Volume (uL):: = 12} ; \
if (step.::Library Prep Kit:: == ::AmpliSeq Library PLUS for Illumina::) {step.::Final Volume (uL):: = 7} ; \
if (step.::Library Prep Kit:: == ::Nextera DNA Flex::) {step.::Final Volume (uL):: = 12} ; \
if (step.::Library Prep Kit:: == ::Nextera Flex for Enrichment::) {step.::Final Volume (uL):: = 10} ; \
if (step.::Library Prep Kit:: == ::TruSeq DNA Nano::) {step.::Final Volume (uL):: = 20} ; \
if (step.::Library Prep Kit:: == ::TruSeq DNA PCR-Free::) {step.::Final Volume (uL):: = 12} ; \
output.::Library Volume (uL):: = (step.::Final Molarity (nM):: * step.::Final Volume (uL)::) / output.::Starting Molarity (nM):: ; \
output.::Library Prep Kit:: = step.::Library Prep Kit:: ; \
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 = 1
Decimal Places Displayed = 0

Final Volume (uL)

Numeric

Read Only

Decimal Places Displayed = 0

Instruction Notes

Multiline Text

Read Only

Default = Select the Library Kit Type and enter in the Starting Molarity before clicking on the Calculate Final & Library Volumes - iSeq button.

Library Prep Kit

Text Dropdown

Required Field
Custom Entries

Presets
- 100% PhiX
- AmpliSeq Library PLUS for Illumina
- Nextera DNA Flex
- Nextera Flex for Enrichment
- Nextera XT DNA
- TruSeq DNA Nano
- TruSeq DNA PCR-Free

Step File Placeholders
- Log - 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

Final Molarity (nM)

Numeric

Derived Sample

Library Prep Kit

Text

Derived Sample

Library Volume (uL)

Numeric

Decimal Places Displayed = 0

Derived Sample

Sample Name

Built-in

Derived Sample

Starting Molarity (nM)

Numeric

Decimal Places Displayed = 0

Project

Project Name

Built-in

Step 2: Dilute Library to Loading Concentration (iSeq 100 v1.0)

Master Step Name = Dilute Library to Loading Concentration - iSeq 100 v1.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Resuspension Buffer (RSB)

Automations

Copy Library Prep Kit & Starting Molarity and Set Loading Concentration - iSeq

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.::Library Prep Kit:: = input.::Library Prep Kit:: ; \
output.::Starting Molarity (nM):: = input.::Final Molarity (nM):: ; \
if (output.::Library Prep Kit:: == ::100% PhiX::) {step.::Loading Concentration (pM):: = 100} ; \
if (output.::Library Prep Kit:: == ::AmpliSeq Library PLUS for Illumina::) {step.::Loading Concentration (pM):: = 40} ; \
if (output.::Library Prep Kit:: == ::Nextera DNA Flex::) {step.::Loading Concentration (pM):: = 75} ; \
if (output.::Library Prep Kit:: == ::Nextera Flex for Enrichment::) {step.::Loading Concentration (pM):: = 50} ; \
if (output.::Library Prep Kit:: == ::Nextera XT DNA::) {step.::Loading Concentration (pM):: = 100} ; \
if (output.::Library Prep Kit:: == ::TruSeq DNA Nano::) {step.::Loading Concentration (pM):: = 125} ; \
if (output.::Library Prep Kit:: == ::TruSeq DNA PCR-Free::) {step.::Loading Concentration (pM):: = 75}' \
-log {compoundOutputFileLuid0}"

Calculate Library & RSB Volumes - iSeq

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.::Library Volume (uL):: = (step.::Loading Concentration (pM):: * step.::Final Volume (uL):: ) / (output.::Starting Molarity (nM):: * 1000) ; \
output.::RSB (uL):: = step.::Final Volume (uL):: - output.::Library Volume (uL)::' \
-log {compoundOutputFileLuid0}"

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

Final Volume (uL)

Numeric

Default = 100
Decimal Places Displayed = 0

Loading Concentration (pM)

Numeric

Decimal Places Displayed = 0

Loading Concentration Notes

Multiline Text

Read Only

Default = Loading concentration ranges: 100% PhiX = 100 AmpliSeq Library PLUS for Illumina = 40-60 Nextera DNA Flex = 75-125 Nextera Flex for Enrichment = 50-100 Nextera XT DNA = 100-200 TruSeq DNA Nano = 125-175 TruSeq DNA PCR-Free = 75-125

Step File Placeholders
- Log - Manually uploaded

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

Library Prep Kit

Text

Derived Sample

Library Volume (uL)

Numeric

Decimal Places Displayed = 0

Derived Sample

RSB (uL)

Numeric

Decimal Places Displayed = 0

Derived Sample

Sample Name

Built-in

Derived Sample

Starting Molarity (nM)

Numeric

Decimal Places Displayed = 0

Project

Project Name

Built-in

Step 3: Add a PhiX Control (iSeq 100 v1.0)

Master Step Name = Add a PhiX Control (iSeq 100 v1.0)
Step Type = No Outputs
Reagent Kits
- PhiX Control v3
  - Supplier = Illumina
  - Catalog Number = FC-110-3001
  - Website = www.illumina.com
- Resuspension Buffer (RSB)

Automations

Copy Library Prep Kit- iSeq

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.::Library Prep Kit:: = input.::Library Prep Kit::' \
-log {compoundOutputFileLuid0}"

Calculate Starting PhiX, RSB & Diluted PhiX 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:http} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false \
-exp 'step.::Starting 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.::Starting PhiX Volume (uL):: ; \
input.::Diluted PhiX Volume (uL):: = (step.::PhiX Spiked In %:: / 100) * step.::Final Diluted 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 Diluted PhiX Volume (uL)

Numeric

Default = 100
Decimal Places Displayed = 0

Final PhiX Molarity (nM)

Numeric

Default = 1
Decimal Places Displayed = 0

Final PhiX Volume (uL)

Numeric

Default = 50
Decimal Places Displayed = 0

Instruction Notes

Multiline Text

Read Only

Default = Combine Starting PhiX Volume (uL) with RSB (uL) to create your diluted PhiX solution.

PhiX Loading Concentration (pM)

Numeric

Default = 100
Decimal Places Displayed = 0

PhiX Spiked In %

Numeric Dropdown

Custom Entries

Presets
- 2
- 10
Default = 2

RSB (uL)

Numeric

Decimal Places Displayed = 0

Starting PhiX Volume (uL)

Numeric

Decimal Places Displayed = 0

Stock PhiX Molarity (nM)

Numeric

Default = 10
Decimal Places Displayed = 0

Step File Placeholders
- Log - 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

Diluted PhiX Volume (uL)

Numeric

Decimal Places Displayed = 0

Derived Sample

Library Prep Kit

Text

Derived Sample

Sample Name

Built-in

Project

Project Name

Built-in

Step 4: Run Setup (iSeq 100 v1.0)

Master Step Name = Run Setup - iSeq 100 v1.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- iSeq 100 i1 Reagent v2
  - Supplier = Illumina
  - Catalog Number = 300 cycle single - 20031371; 300 cycle four-pack - 20031374; 300 cycle eight-pack - 20040760
  - Website = www.illumina.com

Automations

Copy Library Prep Kit- iSeq

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.::Library Prep Kit:: = input.::Library Prep Kit::' \
-log {compoundOutputFileLuid0}"

1. iseq LRM 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/iSeq_Samplesheet.csv \
-o {compoundOutputFileLuid1}.csv \
-q true \
-destLIMSID {compoundOutputFileLuid1} \
-l {compoundOutputFileLuid0}"

2. iseq manual 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/iSeqManual_Samplesheet.csv \
-o {compoundOutputFileLuid2}.csv \
-q true \
-destLIMSID {compoundOutputFileLuid2} \
-l {compoundOutputFileLuid0}"

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

Adapter

Text

Default = CTGTCTCTTATACACATCT

BaseSpace Sequence Hub

Text Dropdown

Presets

Run Monitoring Only
Run Monitoring and Storage

Chemistry

Text

Experiment Name

Text

Required Field

IndexStrategy

Text Dropdown

Required Field

Presets

NoIndex
SingleOnly
DualOnly
SingleAndDual
NoAndSingle
NoAndDual

Library Prep Kit

Text

Local Run Manager Analysis Id

Numeric

Manifest File Name

Text

Module

Text

Output Folder Location

Text

Read 1 Cycles

Numeric

Required Field

Range = 26 To 151

Read 2 Cycles

Numeric

Required Field

Read Type

Text Dropdown

Required Field
Custom Entries

Presets

Single Read
Paired End

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 = 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

Sample Name

Built-in

Project

Project Name

Built-in

PreviousiScan System v1.0 NextMiniSeq v1.0

Last updated 7 days ago