> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/clarity-lims/instruments-and-integrations/iseq-100-v1.0.md).

# 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**

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-39d93e5f27322017ad62ed206c6ac1fa83890149%2Fiseq-next-step-config.png?alt=media" alt=""><figcaption></figcaption></figure>

### 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

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-8f0478e41bc81ae62badd8c033dfbabc225bfac1%2Fiseq-step1-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Calculate Final &#x26; Library Volumes - iSeq</summary>

* Trigger Location = Record Details
* Trigger Style = Manual button

{% code overflow="wrap" %}

```markup
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}"
```

{% endcode %}

</details>

<details>

<summary>Set Next Step - Advance</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon exit

{% code overflow="wrap" %}

```markup
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}"
```

{% endcode %}

</details>

#### 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        |                                                         | <ul><li>Default = 1</li><li>Decimal Places Displayed = 0</li></ul>                                                                                                                                                                             |
  | Final Volume (uL)   | Numeric        | <ul><li>Read Only</li></ul>                             | <ul><li>Decimal Places Displayed = 0</li></ul>                                                                                                                                                                                                 |
  | Instruction Notes   | Multiline Text | <ul><li>Read Only</li></ul>                             | <ul><li>Default = Select the Library Kit Type and enter in the Starting Molarity before clicking on the Calculate Final & Library Volumes - iSeq button.</li></ul>                                                                             |
  | Library Prep Kit    | Text Dropdown  | <ul><li>Required Field</li><li>Custom Entries</li></ul> | <ul><li><p>Presets</p><ul><li>100% PhiX</li><li>AmpliSeq Library PLUS for Illumina</li><li>Nextera DNA Flex</li><li>Nextera Flex for Enrichment</li><li>Nextera XT DNA</li><li>TruSeq DNA Nano</li><li>TruSeq DNA PCR-Free</li></ul></li></ul> |
* 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

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-42ead1c1c4d367bb633a491dc8c47ba78c9e0863%2Fiseq-step2-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Copy Library Prep Kit &#x26; Starting Molarity and Set Loading Concentration - iSeq</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon entry

{% code overflow="wrap" %}

```markup
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}"
```

{% endcode %}

</details>

<details>

<summary>Calculate Library &#x26; RSB Volumes - iSeq</summary>

* Trigger Location = Record Details
* Trigger Style = Manual button

{% code overflow="wrap" %}

```markup
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}"
```

{% endcode %}

</details>

<details>

<summary>Set Next Step - Advance</summary>

* Trigger Location = Not Used

{% code overflow="wrap" %}

```markup
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}"
```

{% endcode %}

</details>

#### 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        |             | <ul><li>Default = 100</li><li>Decimal Places Displayed = 0</li></ul>                                                                                                                                                                                                                        |
  | Loading Concentration (pM)  | Numeric        |             | <ul><li>Decimal Places Displayed = 0</li></ul>                                                                                                                                                                                                                                              |
  | Loading Concentration Notes | Multiline Text | Read Only   | <ul><li>Default =<br>Loading concentration ranges:<br>100% PhiX = 100<br>AmpliSeq Library PLUS for Illumina = 40-60<br>Nextera DNA Flex = 75-125<br>Nextera Flex for Enrichment = 50-100<br>Nextera XT DNA = 100-200<br>TruSeq DNA Nano = 125-175<br>TruSeq DNA PCR-Free = 75-125</li></ul> |
* 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](https://help.bioinsight.illumina.com/clarity-lims/instruments-and-integrations/www.illumina.com)
  * Resuspension Buffer (RSB)

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-24b7fb286dbee9a27aecaed41c9778160c22ad52%2Fiseq-step3-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Copy Library Prep Kit- iSeq</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon entry

{% code overflow="wrap" %}

```markup
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}"
```

{% endcode %}

</details>

<details>

<summary>Calculate Starting PhiX, RSB &#x26; Diluted PhiX Volumes</summary>

* Trigger Location = Record Details
* Trigger Style = Manual button

{% code overflow="wrap" %}

```markup
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}"
```

{% endcode %}

</details>

<details>

<summary>Set Next Step - Advance</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon exit

{% code overflow="wrap" %}

```markup
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}"
```

{% endcode %}

</details>

#### 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          |                | <ul><li>Default = 100</li><li>Decimal Places Displayed = 0</li></ul>                                              |
  | Final PhiX Molarity (nM)        | Numeric          |                | <ul><li>Default = 1</li><li>Decimal Places Displayed = 0</li></ul>                                                |
  | Final PhiX Volume (uL)          | Numeric          |                | <ul><li>Default = 50</li><li>Decimal Places Displayed = 0</li></ul>                                               |
  | Instruction Notes               | Multiline Text   | Read Only      | <ul><li>Default = Combine Starting PhiX Volume (uL) with RSB (uL) to create your diluted PhiX solution.</li></ul> |
  | PhiX Loading Concentration (pM) | Numeric          |                | <ul><li>Default = 100</li><li>Decimal Places Displayed = 0</li></ul>                                              |
  | PhiX Spiked In %                | Numeric Dropdown | Custom Entries | <ul><li><p>Presets</p><ul><li>2</li><li>10</li></ul></li><li>Default = 2</li></ul>                                |
  | RSB (uL)                        | Numeric          |                | <ul><li>Decimal Places Displayed = 0</li></ul>                                                                    |
  | Starting PhiX Volume (uL)       | Numeric          |                | <ul><li>Decimal Places Displayed = 0</li></ul>                                                                    |
  | Stock PhiX Molarity (nM)        | Numeric          |                | <ul><li>Default = 10</li><li>Decimal Places Displayed = 0</li></ul>                                               |
* 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](https://help.bioinsight.illumina.com/clarity-lims/instruments-and-integrations/www.illumina.com)

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-380d8616066b5d4edb6bf394a20f9902b312d8e7%2Fiseq-step4-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Copy Library Prep Kit- iSeq</summary>

* Trigger Location = Record Details
* Trigger Style = Automatic upon entry

{% code overflow="wrap" %}

```markup
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}"
```

{% endcode %}

</details>

<details>

<summary>1. iseq LRM sample sheet</summary>

* Trigger Location = Record Details
* Trigger Style = Manual button

{% code overflow="wrap" %}

```markup
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}"
```

{% endcode %}

</details>

<details>

<summary>2. iseq manual sample sheet</summary>

* Trigger Location = Record Details
* Trigger Style = Manual button

{% code overflow="wrap" %}

```markup
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}"
```

{% endcode %}

</details>

#### 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  |                                                         | <p>Presets</p><ul><li>Run Monitoring Only</li><li>Run Monitoring and Storage</li></ul>                                                  |
  | Chemistry                     | Text           |                                                         |                                                                                                                                         |
  | Experiment Name               | Text           | <ul><li>Required Field</li></ul>                        |                                                                                                                                         |
  | IndexStrategy                 | Text Dropdown  | <ul><li>Required Field</li></ul>                        | <p>Presets</p><ul><li>NoIndex</li><li>SingleOnly</li><li>DualOnly</li><li>SingleAndDual</li><li>NoAndSingle</li><li>NoAndDual</li></ul> |
  | Library Prep Kit              | Text           |                                                         |                                                                                                                                         |
  | Local Run Manager Analysis Id | Numeric        |                                                         |                                                                                                                                         |
  | Manifest File Name            | Text           |                                                         |                                                                                                                                         |
  | Module                        | Text           |                                                         |                                                                                                                                         |
  | Output Folder Location        | Text           |                                                         |                                                                                                                                         |
  | Read 1 Cycles                 | Numeric        | <ul><li>Required Field</li></ul>                        | Range = 26 To 151                                                                                                                       |
  | Read 2 Cycles                 | Numeric        | <ul><li>Required Field</li></ul>                        |                                                                                                                                         |
  | Read Type                     | Text Dropdown  | <ul><li>Required Field</li><li>Custom Entries</li></ul> | <p>Presets</p><ul><li>Single Read</li><li>Paired End</li></ul>                                                                          |
  | 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       |             |                                           |


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation by asking a question.

Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters:

```
GET https://help.bioinsight.illumina.com/clarity-lims/instruments-and-integrations/iseq-100-v1.0.md?ask=<question>&goal=<user_goal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.