Illumina Connected Software refers to Illumina's portfolio of software products, including BaseSpace Sequence Hub, Illumina Connected Analytics, and more.

The following steps represent the end-to-end user journey, from managing workflows in the lab to interpreting data from analyses. Click on each step in the workflow for relevant support provided by Illumina's suite of software solutions.

The roles within a domain that users may be assigned are:

Click on each section below to explore the different features of the Admin Console.

Setting-up Illumina Connected Software

What is Software Setup?

Thank you for purchasing Illumina Software. Illumina Connected Software is made available for your use by completing a software setup process. The process “activates” the software and enables you to assign access to specific persons who will use it. The process has four steps:

1. Click a link in an email provided by Illumina.

3. Identify a software administrator.

4. Configure software settings.

Information You Need to Setup Illumina Software

To setup your Illumina Software subscription or software consumable (e.g. iCredits), you will need the following:

1. An Illumina order confirmation or registration reminder email.

2. Email address of a person who will serve as software administrator
3. Optional: Names of existing Illumina Software workgroups or domains.

Choosing a Software Administrator (Admin.)

Choosing a Software Administrator

The admin email address should be for a person or group that knows enough about your team’s use of the software to provide team members with access to the Illumina Software product(s) when requested.

NOTE: Software administration does NOT require any advanced technical or computer skills.

Software Administration Features

The administration features of Illumina Software are simple. Here are examples of some of the things an administrator can do:

1. Add, remove, and edit user access to Illumina Software Products

2. Organize users into workgroups so they can collaborate

3. Limit login access to specified email addresses

4. Limit login access to specified domains (ex: lucyhealthcorp.com)

5. View the Illumina Software usage reports

Tips for choosing an admin email address

1. Use the same email to register applications if they are purchased as a solution. For example:

   • Illumina Connected Insights can only be accessed if it is setup with the same domain and admin email address used by Illumina Connected Analytics.

2. The administrator email address can be shared by an informatics team, for example sequencingcore@Illumina.com.

3. NOTE: When setting up software on a new domain or workgroup, the email address of the person setting up the software will be used as the admin.

How to Setup Illumina Connected Software

Step 1: Click a link in an email provided by Illumina

Step 2: Access the Software Registration Portal

If you already have a user account for Illumina Software, enter those credentials into the login screen and proceed to step 3 below.

If you do not have a user account, then select the link labeled “Don’t have an account” to create an Illumina user account.

Fig. 2 - Public Domain login page

Step 3 - Identify a Software Administrator

Once you have logged in, you will see the software setup page.

This page is where the software is configured for your use. Here, you assign access to a specific person who will be the software administrator. You will need that person's email address to complete this step.

An administrator is the person who leads or organizes a team of people who are using Illumina Software. An administrator can add or remove users, provide access to specific products, and view software usage data.

Step 3a - Setup software as the software administrator

If you are the person who is going to be the software administrator, proceed to Step 4 below.

Step 3b - Assign another person as an administrator

You should use the button labeled “Assign User" to invite someone else to become software administrator if:

1. Your role is purchasing, or another role unrelated to software.

2. You were sent an Illumina registration email incorrectly.

3. Someone else on your team should be the software admin.

The images below (see fig.5-6) show the button labeled “Assign User" below each order awaiting registration.

When you click the “Assign User" button, a modal window is displayed where you can enter the email address of the person you wish to invite. Press the “Assign” button to send an email to that person containing links to the Software Registration portal.

When that person logs into the Software Registration portal and completes the software configuration steps below, the software is available for use.

Step 4: Configure software settings

Step 4a - View Products Pending Registration

The person identified as software administrator may view and register software orders pending registration (Fig. 7).

Step 4b - Products Pending Registration Details

Each product listed contains two types of information for the user to review or select.

1. Order Detail: This information includes the dates on which the order was placed, the order, number, and the product that was ordered. This data in this section is not editable.

1. "Setup": The section labeled "Setup" contains software settings. Examples of settings are choosing an AWS region, or selecting/creating an enterprise domain that the software instance will be associated with.

<figure><img src="../.gitbook/assets/20241218 StepbyStep_fig9_Large_ICA_v1.2.png" alt=""><figcaption><p><em>Fig. 9 – Setup Details</em></p></figcaption></figure>

Examples of configuration details for specific Illumina software are shown below.

Configuration Examples: How to Configure Illumina Software

There are two types of software that use the setup process:

1. Software Subscriptions

   • Examples:

     • BaseSpace Sequence Hub Professional

     • ICA Professional, ICA Enterprise, Illumina Connected Insights

2. Software Consumables

   • Examples:

     • iCredits, Genome Equivalent Samples

The Software Setup for different types of software are slightly different. The sections below contain three examples that describe how to setup each software type.

Example 1: Setup BaseSpace Sequence Hub Professional

There are two settings to configure for this software subscription:

1. Select the instance region for your subscription

2. Select a Professional Workgroup or Create a New Workgroup

Setting 1 - Select the Instance Region for Your Subscription.

Setting 2 - Select or Create a Professional Workgroup

New and Existing Workgroups

If your login has access to existing workgroups, these are listed on the page for you to choose from. Selecting an existing workgroup will not change the user access on the account. If you do not have existing workgroups, then select the "Create New" menu item and type in the name you prefer (Fig. 11-12). Remember to select the name of the professional workgroup you created so that it appears in your completed configuration (Fig.13).

If the value “Create New” is selected from the dropdown menu, then a modal window is displayed which enables the user to create a new workgroup name.

Press the Register Button

Once the configuration settings have been selected, pressing the register button at the bottom of the order item makes that software available for use. Within 15-30 minutes, you will also receive a welcome notification to confirm the account details.

Example 2: Configuring Illumina Connected Analytics (ICA) Subscriptions

There are two settings to configure for this subscription:

1. Select the Instance Region.

2. Select or Create a Domain.

Setting 1 - Select the Instance Region

Setting 2 - Select or Create a Domain

Press the Register Button

Pressing the register button at the bottom of an order item makes that software available for use. Within 15-30 minutes, you will receive a welcome notification to confirm the account details.

Example 3: Configuring Software Consumables (iCredits or Sample Analyses)

Once a subscription has been setup, then you can select software consumables and add them to your subscription. Examples of software consumables are iCredits or Sample Analyses.

• iCredits are the units that Illumina customers purchase to pay for cloud compute and storage resources they consume in Illumina Software.

• Sample Analyses are the units of software sold with Illumina Product that entitle a customer to perform genomic analyses in Illumina Software. An example of this is Illumina Connected Insights service that provides cloud-based analysis.

There is only one setting to configure for this software consumables:

Setting 1 - Select a Professional Workgroup or Enterprise Domain

Press the Register Button

Once the configuration settings have been selected, pressing the register button at the bottom of an order item makes that software available for use. Within 15-30 minutes, you will also receive a welcome notification to confirm the account details.

Lab management software enables labs to track samples, streamline complex tasks, generate sample sheets, and catch poor quality samples before running them on a sequencing system.

Custom design software helps create custom microarray probes and sequencing panels optimized for specific genomic content of interest. These software tools support a broad range of applications, including custom microarray-based genotyping applications, custom targeted amplicon sequencing, and custom target enrichment.

Workgroups Overview

Workgroups are groups of users that can share projects and data. You can view an overview of the workgroups in your domain by clicking on the "Workgroups" tab. For each workgroup, you will see the following information:

• Collaboration: Indicates whether your workgroup allows collaboration with users outside the domain.

• Description: A description of the workgroup.

• Owner: The owner of the workgroup.

• Created On: The date the workgroup was created.

• Active Workgroup: Selected workgroups are in use. Deselecting a workgroup will permanently delete it, and this action cannot be undone.

Create a Workgroup

Workgroups can be created by domain administrators. To create a new workgroup, click the +New button.

Provide a workgroup name, description, and administrator email. Optionally choose to enable collaborators outside of the domain to add users from other domains to the workgroup. This setting cannot be changed after the workgroup has been created.

Workgroup Details

To view the details of a workgroup, click on the workgroup name. This will redirect you to a screen with additional details outlined below.

From the left-hand navigation menu, you can navigate to the following tabs to view and edit details about your workgroup:

• Admins: Manage administrators, owners, and description of a workgroup

• Users: Manage existing users and invite new users to a workgroup

• Pending Invites: Manage all pending invitations to users of this workgroup

• Applications: Manage user access to applications associated with this workgroup

Admins

In the Admins tab, you will see an Overview screen displaying details of your workgroup. You can update the name, description, and owner of the workgroup by clicking "Change Settings."

In the Administrators section, the names and usernames of the workgroup admins will be listed. The roles of each administrator are also listed below each name.

Invite Admin

To invite a new admin, click the "Invite" button on the right-hand side and enter the email address of the user you want to add. If you would like to add multiple administrators at once, you can specify multiple email addresses with a comma-separated list. Note that the email format must match the Allowed Emails specified in the Domain tab.

Remove Admin

To remove an admin, select the checkbox next to their name and click the "Remove" button on the right-hand side. A popup will appear to confirm whether you want to remove the admin. Leave the box checked to remove the user from all roles in the workgroup. Uncheck the box if you want to keep the user in the workgroup but remove only their admin permissions.

Users

The Users tab will display the total number of users in the workgroup, along with a table listing all the applications each user has access to. This includes all the workgroups the user is part of that have access to different applications. "Has Access" will appear for applications the user can access, while a dash will indicate applications the user does not have access to.

You can click on a user's name to open a detailed view showing which workgroups the user is part of and the applications those workgroups have access to.

Invite User

To invite a user, click the "Invite" button on the right-hand side. This will open a pop-up where you can enter the email address of the user you wish to invite. You can specify more than one email address using a comma-separated list. Note that the email format must match the Allowed Emails specified in the Domain tab.

You can then choose whether the user has access or no access to the different products available to the workgroup. Select the option to "Invite via public Illumina account" if the user you are inviting has a public Illumina account. To invite via collaborative enterprise, you will need to configure the collaboration domains, which can be done under Domain > Collaboration Management. Click "Grant Access" to grant the user access.

Change Access

To change the access for a user or users, select the checkbox next to their name(s) and click the "Change Access" pencil icon on the right-hand side. The emails of the selected users will appear in the Users dialog. Update the applications the users have access to, and click "Grant Access" to save the changes.

Remove User

To remove a user or users, select the checkbox next to their name(s) and click the "Remove Access" icon on the right-hand side. A dialog will open where you can confirm that the user should be removed. Click "Remove" to confirm.

Note that workgroup administrators and owners cannot be removed. These users will be skipped from the list of users to remove, and a warning message will be displayed.

To remove a workgroup administrator or workgroup owner, you must first remove their administrator/owner role. Refer to the "Admins" tab above for instructions on how to do so.

Pending Invites

In the Pending Invites screen, you can see which users have not yet accepted their invites, as well as the applications and roles they would be granted upon accepting their invitation. From here, you can click "Resend Invitation" to send the invitation again.

Applications

Under the Applications tab, you'll see a tab for each application your workgroup has access to. By clicking on an application, you'll see a list of users in the workgroup who have access to it. From this screen, you can invite new users to the workgroup and modify access. See the sections above for information on how to do so.

Manage Domain Access

Cloud Orchestrated Cloud Analysis

The Cloud Orchestrated Cloud Analysis workflow streamlines sequencing run planning and cloud-based secondary analysis using the BaseSpace Sequence Hub Run Planning interface. With Cloud Orchestrated Cloud Analysis, you can plan a sequencing run for a specific instrument platform and configure the associated cloud secondary analysis using the BaseSpace Sequence Hub Run Planning interface. Once the run has been planned, any instrument of that platform can access and kick off the run, provided you log into the instrument using the same workgroup context as the run was planned in.

Sequencing runs using this workflow require you to upload your run data to BaseSpace Sequence Hub so that it can be used to run the associated secondary analysis.

Once the sequencing run is complete and all primary analysis data has been uploaded to BaseSpace Sequence Hub, the secondary analysis is automatically kicked off in the cloud and linked to the run in BaseSpace Sequence Hub.

Cloud Orchestrated Local Analysis

The Cloud Orchestrated Local Analysis workflow enables you to plan your sequencing run (associated with a specific instrument platform) and the associated on-instrument secondary analysis using the BaseSpace Sequence Hub Run Planning interface. Once the run has been planned, any instrument of that platform can access and kick off the run, provided you log into the instrument using the same workgroup context as the run was planned in.

Sequencing runs using the Cloud Orchestrated Local Analysis workflow require you to send at least run monitoring data to BaseSpace Sequence Hub so that the run planned in the cloud can be kept in sync with the instrument.

Once the sequencing run is complete and all primary analysis data has been generated, the secondary analysis is automatically kicked off on the instrument as specified by the user during run planning.

Locally Orchestrated Local Analysis

The Locally Orchestrated Local Analysis workflow enables you to plan a sequencing run and associated on-instrument secondary analysis using the on-instrument Run Planning interface. Once the run has been planned, any user can access and kick off the run upon logging into the instrument.

Once the sequencing run is complete and all primary analysis data has been generated, the secondary analysis is automatically launched on the instrument, as specified by the user during run planning.

Sequencing runs using the Locally Orchestrated Local Analysis workflow enable you to use any level of cloud connectivity and data upload. On NovaSeq X Series or MiSeq i100 Series instruments, you can also optionally upload FastQ and BAM/CRAM files to the cloud if desired.

Manual Run with Sample Sheet Based Local Analysis

The Sample Sheet Driven Local Analysis workflow leverages DRAGEN on the instrument, relying on a sample sheet to provide the necessary details for orchestrating and executing the analysis directly onboard. In order to use this workflow, select the option when setting up a run to perform local analysis using a sample sheet, and attach the desired sample sheet to your run.

When using this workflow, the DRAGEN analysis is started onboard automatically when the sequencing data is in a ready state to begin analysis.

For optimal results, it is recommended to generate the initial sample sheet using the BaseSpace Sequence Hub Run Planning interface for local analysis. This will ensure proper formatting and acceptable values for all fields.

Run set up refers to configuring settings for sequencing on Illumina instruments. In addition, users can provide settings for data analysis, location of the output data, and other parameters.

Sequencing runs can be set up using software applications and by downloading and editing sample sheet templates that are uploaded into the sequencer. The Run Planning tool in BaseSpace Sequence Hub and sample sheets are both generic and support run set-up for a broad spectrum of instruments and analysis pipelines. Other software applications support run set-up and analysis only for specific instruments, assays, and analysis pipelines.

What is a Sample Sheet?

A sample sheet is a comma-separated value (*.csv) file format used by Illumina instruments, platforms, and analysis pipelines to store settings and data for sequencing and analysis. The sample sheet uses American Standard Code for Information Interchange (ASCII) character encoding.

The system using the sample sheet as input validates the data within the sample sheet based on validation rules. Validation rules differ from section to section. Incorrectly formatted data are considered invalid and causes software to throw an error. Refer to the validation rules for each section for more information on acceptable formatting and allowable values.

How to Use a Sample Sheet?

A v2 sample sheet can be obtained from one of the following options.

1. A v2 sample sheet can be created in BaseSpace using Run Planning.

   1. In BaseSpace Sequence Hub, select the Runs tab > New Run > Run Planning > Local Mode > Export Sample Sheet.

   2. For this option, all sample and index information is entered in Run Planning and is included in the exported v2 sample sheet.

2. A v2 sample sheet template can be downloaded and filled out manually.

   1. Download the template with the link below and use a text editor program to alter the sections according to your chosen instrument or analysis. Using a spreadsheet editor can cause errors with sample sheet validation and analysis. Save the sample sheet to a folder accessible by your instrument or analysis software.

   2. Follow instructions to fill out the sample sheet. See resources below:

Overview

The Usage tab provides an overview of the domain's usage. The name of the domain is displayed in the top left of the overview screen.

You can select the month you want to view usage for by using the dropdown menu in the top left corner.

Overall Domain Usage

Total iCredit Balance

The first section will display the total iCredit balance for the domain. This is the current remaining iCredit balance from your purchases. A zero or negative iCredit balance indicates all available iCredits have been used and additional purchases are needed. Additional purchases can be made by clicking the "Purchase More" link.

If you have iCredits purchased through Open PO (also known as consumption billing) payment type, the "Order Expiration" date will be shown. This date indicates when the order will expire, and if it has already expired, any remaining balance will be lost.

If you have iCredits purchased through both Prepaid and Open PO payment types, you'll see a combined iCredit balance, and each iCredit balance for Prepaid and Open PO will be shown separately.

The iCredit usage will be displayed in different colors based on the following categories:

• Compute & Apps: Usage related to processing power and application usage.

• Storage: Usage related to data storage and management.

• Transfer: Usage related to data transfer between services or locations and archiving/unarchiving data.

• Notebook: Usage associated with cloud-based notebooks or computing environments.

• Warehouse: Usage related to data warehousing and analytics services.

Usage Budgets

Usage Budgets allow you to set a Budget Threshold for your Domain and take control of your iCredit spending. To manage Usage Budgets, click the "Manage" button. This will open a popup where you can set up recurring monthly spending limits and receive email notifications when those limits are reached.

iCredit usage will be displayed in different colors based on the amount of credits used and the remaining balance. If you exceed your monthly domain budget threshold, a warning will be displayed.

Application Usage

For each application your domain has access to, you can view the total iCredits used, with categories similar to those in the overall iCredit usage. Use the left-side dropdown menu to toggle between different usage categories and view more detailed information for each.

Below you can find an interactive sample sheet with example values filled out for BCL Convert. Click on the dotted underlines for pop-ups with more information on each section.

Sample Sheet

The orchestration of auto-launched ICA pipelines is driven by information provided in the sequencing run sample sheet. When leveraging BaseSpace Run Planning to plan a run, the sample sheet is automatically generated. The sample sheet may also be attached to the run manually on the sequencer. The following sections are necessary for powering the autolaunch of secondary analysis after the sequencing run completes.

To retreive the most up-to-date sample sheet template for your instrument, generate an example using BaseSpace Run Planning.

Use Run Planning to Export a Sample Sheet

1. Log into your BaseSpace Sequence Hub account.

2. Select the Runs tab, and then select the New Run drop-down.

3. Select Run Planning.

4. In the Run Name field, enter a unique name of your preference to identify the current run. The run name can contain a maximum of 255 alphanumeric characters, spaces, dashes, and underscores.

5. Optional: Enter a description for the run. The run description can contain a maximum of 255 characters.

6. Select your sequencing system as the instrument platform.

7. For Secondary Analysis, Select BaseSpace.

   1. Note that if you have an ICA subscription, this option will read BaseSpace / Illumina Connected Analytics.

8. Optional: Enter the ID for your library tube. The library tube ID is located on the label of your library tube strip.

9. Select Next.

10. Select your analysis application. If only one option is available, it will be selected automatically.

11. Optional: Enter a description for the configuration.

12. Select an existing library prep kit, or add a new custom library prep kit as follows:

    1. Select Add Custom Library Prep Kit under the Library Prep Kit dropdown.

    2. Enter the name, read types, default read cycles, and compatible index adapter kits for your custom library prep kit.

    3. Select Create New Kit.

13. Select an existing index adapter kit, or add a new a custom index kits as follows. If you are using more than one library, the libraries must have the same index read lengths.

    1. Select Add Custom Index Adapter Kit under the Index Adapter Kit dropdown.

    2. Select a template type and enter the kit name, adapter sequences, index strategies, and index sequences. Make sure the second index (i5) adapter sequences are in forward orientation.

    3. Select Create New Kit.

14. If applicable to your application, select a reference genome.

15. Select Next to configure secondary analysis settings. Detailed instructions for each application and version can be found here.

16. Select Next to review the Run and Analysis details.

17. Select Export to save the Sample Sheet to your device.

The FileFormatVersion in the [Header] section must be set to 2 to indicate the sample sheet as v2 format.

[Header],
FileFormatVersion,2

Sample sheets generated using BaseSpace Run Planning may contain additional optional header fields such as RunName, InstrumentPlatform, and IndexOrientation.

Primary Analysis Settings

The primary analysis settings consist of the information used for the on-instrument sequencing and demultiplexing of raw sequencing output data. This includes information about reads, indices, primers, etc.

These sections vary greatly depending on the instrument type used and sequencing configuration. The below examples are used for demonstration purposes only.

[Reads],
Read1Cycles,1
Read2Cycles,1
Index1Cycles,1
Index2Cycles,1

[Sequencing],
CustomRead1Primer,false
CustomRead2Primer,false
CustomIndex1Primer,false
CustomIndex2Primer,false

[BCLConvert_Settings],
SoftwareVersion,0
BarcodeMismatchesIndex1,
BarcodeMismatchesIndex2,
AdapterRead1,
AdapterRead2,
OverrideCycles,

For demultiplexing the raw sequencing output data, the settings for demultiplexing (ie, BCL Convert) are included. The below examples are used for demonstration purposes only.

[BCLConvert_Settings],
Sample_ID,NS001
Index,T
Index2,A
Lane,1

Secondary Analysis Settings

A [Cloud_<pipeline_name>_Settings] and [Cloud_<pipeline_name>_Data] setting are provided for each secondary analysis pipeline to be auto-launched after sequencing. The value used for <pipeline_name> can be any value. It's best practice to refer to the analysis type such as "DragenGermline", "BCLConvert", etc. These sections provide input parameters to the pipelines. The contents of these sections, including the columns, may vary depending on the pipeline used for secondary analysis. The below snippet demonstrates using "DragenGermline" as an example.

[Cloud_DragenGermline_Settings]
SoftwareVersion,4.1.5
MapAlignOutFormat,bam
 
[Cloud_DragenGermline_Data]
Sample_ID,ReferenceGenomeDir,VariantCallingMode
<sample_id>,urn:ilmn:ica:region:<region_guid>:data:<data_guid>#<data_path>,None
<sample_id>,urn:ilmn:ica:region:<region_guid>:data:<data_guid>#<data_path>,None

The [Cloud_Settings] section must be present and include:

1. Cloud_Workflow value set to ica_workflow_1

2. BCLConvert_Pipeline set a valid ICA Uniform Resource Name (URN) for demultiplexing

   1. Note: To find secondary analysis URNs for a specific pipeline, click on the pipeline in the Pipelines section in ICA, and view the Information tab.

3. [Optional] One or more Cloud_<pipeline_code>_Pipeline entries set to a valid ICA URN for secondary analysis.

[Cloud_Settings]
GeneratedVersion,0.0.0
Cloud_Workflow,ica_workflow_1
BCLConvert_Pipeline,urn:ilmn:ica:pipeline:<pipeline_uuid>#<pipeline_code>
Cloud_DragenGermline_Pipeline,urn:ilmn:ica:pipeline:<pipeline_uuid>#<pipeline_code>

The Illumina Usage Explorer allows you to track your usage costs across Illumina cloud products with detailed insights and trends.

Overview

Summary

The summary section gives you a quick look at your iCredit balance, iCredit usage for the current month, quarter, and year, and total storage separated by tier. If you have purchased or used cost units other than iCredits (e.g., GEs, Samples, etc), they will be displayed under additional tabs.

Domain admins can set a budget threshold, and if set it will display in the summary section. To set a budget threshold, switch on the budget notifications toggle and click "Edit budget settings" to specify an iCredit threshold and any email recipients.

Trend & Details

The Trend & Details section gives you the ability to filter, group, and explore your usage. The controls on the right side have a variety of options that allow you to examine your data at the granularity you choose. Above the chart, usage and storage metrics are displayed that update with the filter settings.

Below the chart, a table summarizes the data and can be exported as a CSV file. The usage shown depends on several factors including your subscription and admin status. For example, a domain admin has access to all domain usage, including users, workgroups, and ICA projects, while a workgroup or ICA project admin has access to usage within that specific workgroup or project, respectively.

Reports

The reports tab allows you to download a CSV-formatted report of your usage costs for a given time period. Use the date choosers to select a range for the report, up to three months at a time.

By default, the reports are generated in the latest usage report format. This newer format is more detailed, but the legacy option is also available to preserve backwards compatibility.

• Blank = Not supported

Overview

The Domain section displays domain usage and allows you to manage permissions at the domain level. Please refer to the sections below for more information on each tab.

Usage Report

The Usage Report section allows you to generate various usage reports.

You can choose from the following report options:

You can select the days you want to include in the Usage report. Enter the email addresses of the users you wish to send the report to. A notification will appear, letting you know that the report will be sent to your email once it's complete.

Password Management

In the Password Management section, you can configure different requirements for the passwords users generate when accessing the domain.

Strength of Password

These settings are designed to ensure passwords are as strong as possible.

• Choose a minimum password length between 8-10 characters.

• By default, the option to require one or more special characters is selected.

• By default, the option to require at least one digit is selected.

• By default, the option to require both lowercase and uppercase letters is selected.

Account lock-up

These settings control locking the account after too many unsuccessful login attempts.

• Max unsuccessful tries: Choose the number of failed login attempts that will trigger an account lock.

• Reset time for lock-up account: Choose the amount of time a user's account will remain locked after the specified number of incorrect password attempts before they can try logging in again.

Password re-use check

This setting ensures that a user cannot reuse the same password too many times. Users will be required to set a new password within a set period.

• Select the number of days to look back when checking for previously used passwords. For example, if you set this to 30 days, passwords used more than 30 days ago can be reused when a user is required to set a new password.

• Choose the number of last-used passwords that should not be allowed as a new password.

Password policy

The password policy is a text message displayed as an alert during the password selection process on the registration page.

Session Management

In the Session Management section, you can configure settings for a user's session and inactivity timeout.

Idle session and JWT

These settings allow you to configure the idle session timeout and JWT expiration time.

• User's idle session timeout in minutes: Set the number of minutes a session can be idle before it times out. An idle session is one where the user is not actively interacting with the session. For example, if a user is working in a different tab and does nothing in their session, this would be considered an idle session. Accepted values are 5-60 minutes. To disable session timeout, set this value to -1.

• JWT expiration time in minutes: This setting determines the duration before the JWT token expires. The JWT (JSON Web Token) is used for securely transmitting information between parties, often for authentication and authorization purposes. It contains claims (such as user information) and is used to verify the user's identity for access to resources. Accepted values are 120 to 10,080 minutes (2 hours to 7 days).

User API Key

These settings allow you to configure the expiration and active limit for the API key.

• API Key expiration time in days: Set the number of days before the API key expires. To disable API key expiration, set this value to -1.

• Active API Key limit: Set the maximum number of active API keys that can be used at the same time for a user. This helps manage the number of concurrent API sessions a user can have, ensuring that resources are not overwhelmed by too many simultaneous requests.

User Management

In the User Management section, you can manage users, administrators and service accounts.

Users

In the Users tab, you can view a list of all domain users. You can search for a specific user using the search bar at the top.

Click "Manage" next to the user to view more details below the overview table, including information about the user's state and API keys.

In the User State overview, you can view details about the user and expire the account by selecting the "Expire User" checkbox.

In the User API Keys overview, you can view details of the user's API keys, including the name, status, creation date, expiry date, and the last time the key was used. To delete an API key, click the "Delete" button. Click the three dots next to the "Delete" button to view the roles associated with the API key. Make sure to click "Save" to apply any changes.

Allowed Emails

In the Allowed Emails tab, you can specify which email addresses are allowed to join the domain. To add an email, type the emails or email suffixes, separated by commas, and click the "+" icon. Any allowed emails will appear at the bottom. To remove an email, click the red "X" next to it.

Allowed Email Suffixes: This option allows users to join the domain if their email contains a specified allowed suffix. Do not include the "@" symbol. It is not recommended to allow common email suffixes, such as gmail.com.

Allowed Emails: This option allows users to join the domain if their email exactly matches one of the allowed emails.

Administrators

The Administrators tab is used to manage the domain's administrators. You can view an overview of the names and emails of users who are currently administrators of the domain. To remove an administrator, click the "Remove" button on the right.

To add or promote a user to an administrator role for the domain, click "Configure an Administrator," then enter the email address of the user and click "Check." You can then fill out the form and click "Save" to assign the user as an administrator.

Domain Invitation

In the Domain Invitation tab, you can add one or more user emails to invite them to the domain. Be sure to separate the emails with a comma. Click "Invite" to send the invitations. An overview table will display each user's username, email, and the status of whether they have accepted the invitation. You can revoke their invitation by clicking the "Revoke" button.

Service Accounts

In the Service Accounts tab, you can view the service accounts that have access to your domain. Service accounts are special accounts used by applications or services to interact with your domain without requiring a user to log in.

Click the checkbox to block service accounts if you want to disable existing service accounts and prevent the creation of new ones.

You can click "Manage" next to a service account to view more details below the overview table, including information about the account state and API keys. In the Account State overview, you can view details about the service account, such as its activation and expiration dates. Click the checkbox to expire the service account.

In the API Keys overview, you can view details of the account's API keys, including the name, status, creation date, expiry date, and the last time the key was used. To delete an API key, click the "Delete" button. Click the three dots next to the "Delete" button to view the roles associated with the API key. Make sure to click "Save" to apply any changes.

Access Management

In the Access Management section, you can set IP addresses or CIDR blocks to restrict access to the application to only the specified addresses.

Using IP range-based authentication, you can control access by IP address, allowing or blocking access to specific addresses or ranges of addresses. Examples include 192.10.10.1, 192.255.10.*, or 192.10.10.0/32. Be sure to separate multiple addresses with commas.

Select a preferred method of access management:

• Create an allow-list for IP addresses/CIDR to allow access: The IP addresses/CIDR block ranges you enter will be allowed access to the domain.

• Create a block-list of IP addresses/CIDR to block access: The IP addresses/CIDR ranges you enter will be blocked from accessing the domain.

Authentication

In the Authentication section, you can configure the authentication type.

Single Sign-on (SSO)

To enable logging into the platform using your organization's identity provider (IDP), a SAML configuration may be provided in your account settings.

Prerequisites:

• Must be configured with an tenant administrator account for your Illumina enterprise domain

• Access to your IDP system to configure the Illumina Service Provider

• Your IDP configurations

  1. Metadata XML

  2. SAML Attributes for EmailId, firstName, LastName

Setup Instructions

1. Navigate to the domain tab and choose the authentication menu item on the left pane. Change the Authentication Configuration to "SAML".
2. Upload your IDP Metadata XML file.
3. Register the Illumina Service Provider (SP) in your IDP system by downloading the illumina_sp.xml file.
4. Enter the relevant IDP/SAML attributes (Contact your organization's technical support team for these details).

Allow 15 minutes for the Illumina Service Provider to update with the provided information. To confirm SAML configuration changes, go to the domain login URL https://<domain>.login.illumina.com. This should now redirect to the configured IDP login page.

Collaboration Management

In the Collaboration Management section, you can configure the collaboration domain namespaces.

This allows you to invite users to a workgroup via Collaborative Enterprise. Enter the domain namespace and click the + button to add it.\

Role Management

In the Role Management section, domain admins can create and manage custom roles with unique permission settings that provide access control within workgroup.

You can search by application name or role name at the top. In the overview table, you'll see a list of applications along with their associated roles. You can click on each role to view detailed information via a hyperlink.

To create a new role, click the "Create role" button. Select an application from those available for custom roles, enter role name and a role description (optional), and select at least one permission for setup. You can edit the role after saved. Selecting application is not available for editing.

Multi-Factor Authentication

In the Multi-Factor Authentication section, you can enable Multi-Factor Authentication (MFA) for the domain by selecting the checkbox.

Allowed Days to skip MFA setup

You can specify the number of allowed days to skip MFA setup. This means users will have a grace period (specified number of days) to complete their MFA setup before it becomes mandatory.

Max unsuccessful tries

You can also set the maximum number of unsuccessful attempts from the dropdown menu. This controls how many failed MFA attempts are allowed before further actions, such as account lockout or additional security measures, are triggered.

Note: Usage reports can only be generated for the last 90 days. For any information older than 90 days, please contact Illumina Support.

Q: What types of Illumina Software require registration?

A: There are two types of software that use the registration process to activate:

• Software Subscriptions

  1. BaseSpace Professional Subscriptions

  2. ICA Professional, ICA Enterprise, Illumina Connected Insights Subscriptions

• Software Consumables

  1. Examples: iCredits, Genome Equivalent Samples, Illumina Complete Long Reads cloud analysis, Consumption billing

Q: Why is selecting professional workgroups or enterprise domains required?

A: Workgroups and Domains are used by some Illumina Software to control access to different customer’s data and assets. Examples of a domain are dcehealth.Illumina.com or coreseqinc.Illumina.com. Choosing a domain is required when registering Base Space Enterprise, ICA, or Cohorts Subscriptions. Here is a description of how workgroups and domains are used by Illumina Software.

Q: Why do I not see my orders listed on the Order Registration page?

A: If you arrive at the Software Registration Portal page and see no orders listed, this means that the orders have not been associated with your email address.\

Q: I completed my registration, why cannot I access my software?

A: After registration is completed, a notification will be sent to your email address to confirm the account details.

NOTE: Provisioning of your software in the cloud can take up to 15-30 minutes after registration is complete. When provisioning is completed, you will receive a welcome notification that includes getting started information about your subscription.

Q: What are the system actions and notifications that are enabled for the software administrator when they register software?

The information contained within a sample sheet is organized into various sections, like Header, Reads, Manifests, Data, and Settings. There are two types of sections:

Standalone sections—Contain run settings and data that do not pertain to a specific application.

Applications sections—Contain run settings and data required by specific applications.

Standalone Sections

The Header and Reads sections contain run settings and data. The Header and Reads sections are present in every v2 sample sheet. Additional standalone sections such as Sequencing Settings can be added and do not produce an error.

A new section includes a section header that precedes the data contained within the section. A section header consists of the name of the section within brackets, as seen in the first line of the following example.

Application Sections

Designate an applications section by appending Settings or Data to the section name as seen in the following example.

Each application can have a maximum of one Settings section and one Data section.

Settings section—This section contains key-value pairs that configure settings for the application, as seen in the example. The Settings section is applied globally to all samples.

Data section—This section contains per sample data (in tabular format) used as input by the given application. The data in the first non-empty line of the application data section forms the column headers for the rest of the section. The Data section is uniquely applied to each sample.

This table describes how to enter the i5 sequence, Forward (F) or Reverse Complement (RC), depending on the instrument and software used.

Guidelines for reverse complementing i5 sequences for demultiplexing

When performing dual indexing, all Illumina sequencers read the first index (i7) in the same direction; however, the second index (i5) is read in different orientations depending on the instrument and chemistry, in particular, differences between when the paired-end turnaround and i5 read take place:

• On the MiSeq, HiSeq 2000/2500, and the MiniSeq Rapid kits the i5 sequence is read in the forward orientation.

• On the iSeq 100, MiniSeq, NextSeq 500/500, NextSeq 1000/2000, HiSeq 3000/4000/X systems, NovaSeq 6000 (v1.5 reagents), and the NovaSeq X/X Plus the i5 sequence is read in the reverse complement orientation.

When demultiplexing, the final sample sheet provided to the FASTQ generation software needs to have the i5 index in the correct orientation for that platform. However, most Illumina sample sheet generation software handles this automatically. This means that these software work on the assumption that your i5 sequence is always in the forward orientation and will automatically create the reverse complement of the sequences provided for the appropriate instrument type.

The following provides guidance on when to reverse complement and when to not reverse complement the i5 sequences when analyzing iSeq, MiniSeq, NextSeq 500/550, NextSeq 1000/2000, HiSeq 3000/4000/X, NovaSeq 6000 (v1.5 reagents), or NovaSeq X/X Plus data.

Important Caveats for MiniSeq Rapid Kits

• The MiniSeq Rapid made a recipe change that uses the grafted oligo for the i5 index priming, so it is read in the forward orientation similar to a MiSeq.

• If running in manual mode and using bcl2fastq or BCL Convert, or uploading the sample sheet to BaseSpace as a manual mode run and attaching a sample sheet, enter the i5 sequence in the forward direction. Runs uploaded in manual mode have their data directly passed to bcl2fastq with no further processing.

• For Local Run Manager (LRM), input the sequences in the reverse complement when setting up the run so the software automatically creates the forward orientation as needed for analysis. This is the opposite of most of our guidance and is only for the MiniSeq Rapid kits.

Color Balance Considerations

When assessing index sets for color balance, the sequence observed by the instrument must be assessed, regardless of the orientation used for the sample sheet. For the i7 index, always asses color balance using the "i7 bases for sample sheet" column orientation. For the i5 index, assess color balance using the forward orientation for MiSeq runs and MiniSeq runs with rapid reagents, and the reverse-complement orientation for all other instruments.

Which orientation are the indexes in Top_Unknown_Barcodes output from BclConvert?

For The NextSeq 1000/2000 and NovaSeq X/X Plus platforms, the RunInfo.xml file includes the IsReverseComplement flag. With this flag, the index sequences that BCL Convert recognizes and outputs are in the following orientations in the Top_Unknown_Barcodes output file.

• Index 1: the i7 index column is in the forward orientation (match the orientation if the i7 indexes in the sample sheet).

• Index 2: the i5 index column is in the reverse complement orientation (are the reverse complement of the i5 indexes in the sample sheet).

For all instruments, the indexes shown in the Top_Unknown_Barcodes are the sequences as they were sequenced/read by the sequencer.