Illumina Knowledge Illumina Support Sign In

iSeq 100 Run Setup v1.0

PreviousiScan System v1.0 NextMiniSeq v1.0

Last updated 3 months ago

Was this helpful?

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