Once you're inside an application, you can return to Connected Home at any time by clicking on the waffle menu present to the top right corner and selecting "Platform Home." From the waffle menu, you can also switch between any of the applications you have access to.

The left navigation menu in Connected Home provides various options to manage account in Illumina.

Usage

The Illumina Usage Explorer allows you to track your usage costs across Illumina cloud products with detailed insights and trends. To learn more about the usage explorer visit Usage Explorer.

User

In the left navigation menu, the User component features a dropdown list containing options for managing the following:

• Profile

• API keys

• Sessions

• Passwords

• Communications

Profile

The "Profile" option takes you to a page where you can update your profile information. Please note that the email address associated with your profile cannot be changed. However, you can edit the following fields: first name, last name, company name, job title, and country/region.

Click "Save" to apply your changes, or "Cancel" to discard them.

API Keys

The "API Keys" page allows you to view and manage all your API keys.

Manage Existing API Keys

You will see a list of all the API keys associated with your domain, including their status, creation date, expiration date, last used date, and available actions. You can expand the dropdown for each key to view the roles associated with it, if applicable.

Click the icon to generate a new version of an existing API key. Regenerating an API key creates a new key value that replaces the old one. This is often done for security reasons—such as when you suspect a key has been exposed—or to rotate credentials regularly. Please note: if you regenerate a key, any existing integrations that rely on the original key may stop working unless you update them with the new key.

Click the icon to edit an API key. You can update the key name and choose whether the changes apply to all future workgroups and roles within the domain. You can also specify which current workgroups and domains the updated name applies to.

Click theicon to delete an API key. You can no longer access the API key once it's deleted.

Generate New API Key

To create a new API key, click the "Generate" button. Provide a name for the key, then choose to either include all workgroups or select specific workgroups that the key should have access to.

Once generated, the API key will be displayed in a hidden format. Use the "Show Key" button to reveal it, and optionally download the key as a file for secure storage.

⚠️ Important: Once this window is closed, the key will no longer be accessible through the domain interface. Be sure to store it securely for future use.

After generating a key, keep it in a safe location to use when accessing the platform via the command-line interface (CLI) or APIs.

Sessions

The "Sessions" page takes you to a table displaying a log of your user account session activities. Activities such as sign-ins, session generations, and sign-outs from different devices are recorded.

You’ll also see additional columns providing details about each activity, including the device, browser, IP address, creation time, last activity time, and action.

From the Action column, you can click "Sign Out" to end any active sessions.

Lastly, click the waffle menu next to each column header to pin, autosize, reset, or customize the ccolumns displayed.

Password

The Password page allows you to change the password for the domain.

Communication

The Communication page allows you to choose the communication preference from Illumina

Subscriptions

The "Subscriptions" link takes you to a table displaying all subscriptions associated with the domain. This includes details such as the subscription name, subscription number, status, start date, end date, email address, and available actions.

The end date indicates when the subscription is scheduled to expire.

Most subscriptions—such as ICA—provide access to applications for all users in a domain.

For certain subscriptions—such as ICM—specific users need to be assigned to the subscription in order for someone to access the associated application. Only domain admins have permission to assign or unassign users to these type of subscriptions. To assign a user, click "Assign" and enter the user’s email address.

To unassign a user, click the "Unassign" link and the user will be removed.

Click the waffle menu next to each column to filter, pin, autosize, reset, or customize the columns displayed.

Orders

The Orders Registration page allows you to set up and manage software orders. To learn more about the Order Registration and Software setup visit Software Setup.

Admin

The Illumina Admin console is a platform designed for administrators to manage product usage, control workgroup permissions, and oversee domain access. To learn more about the Roles, Workgroup and Domain visit Admin console.

Accessing Orders Page

If you already have a user account for Illumina Connected Software, enter those credentials into the login screen. If you do not have an Illumina user account, then select the "Sign up" link to create a new account. You should choose this option if this is the first time you have registered through the Order Registration Portal.

Once you have logged in, you will either be directed straight to the Order setup page (if you created a new account), or you will see your Connected Home page (if you are logging into an existing account).

To access the Orders page from the Connected Home page, select "Orders" from the left navigation menu.

Once you have made it to the Order Registration page, you should see a table displaying all the orders that need to be registered. This includes details such as the Product name, Setup status, Order date, order number, Customer id, Assignees.

Order Registration

If you’ve been given an order code, you can enter it using the "Enter order code" option at the at the top right corner above the table. This will add the order to your account so you can proceed with registration.

Assign additional users to set up the software (Optional)

For each order awaiting registration, you can assign specific users to set up the software. Click the button “Manage" under Assignees column, a modal window is displayed where you can view the users currently assigned to the order.

To add a new Assignee, you can enter the email address of the person you wish to invite and click "Add". Press the “Confirm” button to send an email to that person containing a link to the Order Registration portal. To remove someone, click the X next to their email address and press "Confirm".

Configure software settings and set up the software

Review Order Details

You can review the "Order details" for each order by clicking on the "Order number" link in the table. This information includes the date the order was placed, the order number, the purchaser email, the subscription term, and other key informations about the order. This information is not editable.

Set Up the Software

To set up the order, select the order you want to setup and click on the "Setup" option next to the "Enter order code" at the top right corner above the table.

You can select multiple orders to set them up at once. The "Setup" option contains software settings. You will need to select a region and domain/workgroup to which the software will be registered. The domain and region cannot be easily changed after the setup is complete.

Select a Region

First, select the region where the software will be registered. This determines the AWS Region in which your software will be installed and run. It is best practice to choose a region that is geographically close to where the software will be used. Most subscriptions are regional and require selecting a region, but consumables (e.g., iCredits) are not, so this step will be skipped for them.

Select a Domain/Workgroup

Next, select the domain or workgroup to which the software will be registered.

If the account you're logged in with has access to existing domains or workgroups, they will be listed on the page for you to choose from. Selecting an existing domain or workgroup will not affect or modify user access permissions associated with that account.

If you do not have existing domains or workgroups, then select the "Create a new domain" or "Create a new workgroup" button (depending on the type of order you are registering).

Create a New Domain

Upon clicking "Create a new domain", a modal window will be displayed where you can enter the following details for your domain:

• Name: Nickname for domain that is unique and easy to identify (ex. “My Company Name’s Domain”). You may only use lowercase alphanumeric, dash (-), max 50 characters and no spaces.

• .

Click "Setup" to create the domain. Make sure to select the name of your domain once it's been created.

Complete the Setup

Once the configuration settings have been selected, press the button at the bottom of the order item to make the software available for use. Upon clicking this button, you will no longer be able to access or modify the order in the Order Registration Portal.

you will receive a welcome notification that includes getting started information about your subscription

At this point, all users in the domain or workgroup should be able to access the software from Connected Home. However, if you have a software which requires adding specific users to the subscription before someone can access the associated application—such as ICM—you can navigate to the Subscriptions page to assign users.

If you have a software which requires every user to be part of a workgroup before they can access the app—such as ICI, Emedgene, and ICM— you can navigate to the Admin Console to create workgroups and add users to the workgroup.

From the Admin Console, you can also assign different domain admins.

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.

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

The application sections contain data required to run Illumina applications. Application settings differ from instrument to instrument. Refer to the applicable instrument settings section.

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.

Q: Why is selecting workgroups or 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 BaseSpace Enterprise, ICA, or Cohorts Subscriptions. Choosing a workgroup is required when registering BaseSpace Professional. Software consumables (such as iCredits) can be applied to either domains or workgroups of active subscriptions.

Below 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.\

You have most likely been forwarded an Illumina registration email and clicked on the link to get to the registration portal. The portal does not recognize your email because the person that forwarded the message did not request that your email be assigned to register new products.

The solution for this is to ask the person who forwarded the email to you to log into the registration portal and add your email address using the “Assign User” button. If this does not resolve the issue or you are unable to locate your order after logging in, please contact [email protected] or click on the FAQ link on the Registration Page.

Q: I completed my registration, why can I not access my software?

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

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.

Set Up Sequencing Run with Cloud Analysis Sample Sheet

1. From the Home screen, select Sequence.

2. From the Run Setup Option screen, select Manual.

3. From the BaseSpace Options screen, select Use BaseSpace™ Sequencing Hub for this run.

   1. Select the Run analysis, collaboration, and storage option to send all run data to BaseSpace Sequence Hub.

   2. Enter your BaseSpace Sequence Hub account credentials.

   3. Select Sign In.

   4. Select the Workgroup.

4. Select Next.

5. Set the Read Type, Read Length and Custom Primers for all of your cycles.

6. Browse to select your sample sheet file. See for information on how to download a sample sheet file.

7. Select Next.

8. Continue to set up the sequencing run as per the .

Roles

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

Get Started

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

CombinedIndexCollisionCheck,value Where value corresponds to the number of the lane or lanes to use this behavior; multiple lane values should be semicolon-separated.

• 4.1.7 and 4.2.x: Relaxed mode by default. CombinedIndexCollisionCheck removed. Mode now configured by using sample sheet option:

IndependentIndexCollisionCheck,value to allow optional strict checking, where value corresponds to the number of the lane or lanes to use this behavior; multiple lane values should be semicolon-separated.

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." The workgroup owner will automatically be added as a workgroup administrator and user if not already. They are the primary administrator and main point of contact for users within the workgroup.

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

To manage domain access, click the "Manage Domain Access" button. This will redirect you to the Domain tab. For more information on domain management, refer to the Domain section.

• Added Platform Home section with information about Managing API Keys, Subscriptions and more.

• Updated Software Setup docs to reflect changes in software registration process.

2025 February 17

• Added Usage Explorer section with information on how to navigate the new tool and track usage across products.

2025 January 6

• Updated Sample Sheet documentation.

  • You can now view sample sheet parameters and definitions by selecting your instrument under the "Instrument Settings" section, choosing the desired pipeline from the right navigation panel, and selecting the appropriate version.

  • Added a BCL Convert Interactive Sample Sheet, allowing users to click on different parameters to view detailed explanations of each.

  • Included an and to clarify which i5 sequence orientation to use for different platforms, based on the analysis software.

  • Added information about various and their compatibility with different instrument platforms.

  • A new "" section provides additional information on , , and a comprehensive .

• Updated documentation

• Added information on the /IAM Console.

2024 December 11

• Updated Sequencer Auto-Launch Analyses Compatibility table

2024 October 25

• Updated Sequencer Auto-Launch Analyses Compatibility table

• Added Secondary Analysis Troubleshooting information for analyses not showing up in ICA

2024 September 4

• Updated Sequencer Auto-Launch Analyses Compatibility table

2024 August 2

• Added links to Custom Design Products

• Updated user documentation links

• Updated Cloud Analysis Auto-Launch page to include instructions for viewing sequencer run data and analysis in BaseSpace

• Made changes to page to include updated information for requeuing an analysis in BaseSpace

• Updated table

• Added page in Reference section

2024 June 25

• Initial release

• Added Software Registration instructions and FAQ

• Added links to all documentation sites in the Illumina Connected Software suite

• Added instructions

• Added for MiSeq

• Added comprehensive guide for performing

• Created table with guidance on sequencer compatibility with different versions of DRAGEN secondary analysis pipelines and applications with auto-launch capabilities

• Added with step-by-step instructions for performing downstream analyses and interpretation in the Cloud

Ensure you purchase the correct samples for your workflow requirements.

Illumina software products and usage pricing overview

Below are the Illumina software products and their software usage pricing details:

Billing Model Overview

Platform Usage

All software usage is eligible for charging. This includes any compute, storage, data transfer, or other metered activity associated with your account.

We recommend that you regularly review your usage and understand how costs accrue, both in one-time costs, such as compute events, or ongoing, such as storage. You are responsible for stopping usage and deleting any data/storage you no longer want to pay for.

Usage Tracking

The Usage Explorer is your central tool for managing and optimizing software consumption at Illumina. It helps you to:

Monitor Usage in Real Time

• Track how iCredits or samples are consumed across various products and projects.

Manage Billing Balances

• Easily view Pre-Funded and Post-Paid balances at a glance to always stay informed.

Audit and Forecast

• Access detailed monthly usage statements.

• Generate custom usage reports to analyze trends, forecast future needs, and prevent unexpected costs.

Optimize Behavior

• Identify high-usage patterns and adjust workflows to remain within budget.

How software usage is billed

Software usage requires a subscription and can be billed through either monthly invoicing or pre-funded credits. Software usage differs based on software products and usage types.

iCredits Billing

We offer two billing options for iCredits.

1. Post-Paid (Monthly Invoicing) Billing:

• You pay for usage after the occurs, billing is in monthly arrears.

• This is the default billing method.

• Invoices are sent to the Bill‑To contact on your account—typically your organization’s Finance or Accounts Payable team, or another designated recipient. Some customers also receive invoices through portals like Ariba or Coupa, depending on their setup. If you need to update the Bill‑To contact or add additional recipients, Support/Customer Care can assist.

• If you do not purchase or contract any pre-funded iCredits in advance, your usage will be billed automatically at the end of the month.

• If your pre-funded iCredits run out (balance reaches zero), billing will switch to post-paid automatically.

2. Pre-Funded Billing:

You purchase or contract for iCredits in advance and draw down from your balance as you use them. There are two ways to pre-fund.

• Pre-paid iCredits

  • You purchase a fixed amount of iCredits upfront. To view purchasing options for iCredits click here

  • Usage reduces your balance until it reaches zero.

  • Before your balance runs out, you’ll need to buy more iCredits or your account will switch to Post-Paid billing automatically.

• Open Purchase Order iCredits

  • You contract for a set quantity of iCredits with an expiration date. To view purchasing options for iCredits

  • A new Open Purchase Order is required when:

Sample Billing

Only available through pre-funded billing.

• Pre-paid Samples

  • You purchase a fixed amount of Samples upfront.

  • Usage draws down from your balance until it reaches zero.

  • When your balance runs out, you’ll need to purchase additional Samples to continue usage.

Post-Paid iCredit Billing + Pre-Paid Sample Billing

When your account uses iCredits (Post‑Paid / Monthly Invoicing) and Prepaid Samples together, your usage is billed in two parallel streams, depending on the product type.

• Usage Explorer

  • A unified view of your overall software usage.

  • Balances:

    • iCredits (Post‑Paid): Shows estimated month‑to‑date charges that will appear on your monthly invoice.

    • Samples (Prepaid): Shows your remaining Sample balance and the usage drawdown for Sample-based products.

• End‑of‑month invoice

  • iCredits: All usage metered via iCredits for the previous month will be billed in arrears

  • Samples: There is no invoice for Sample usage.

How transitioning between billing options works

Illumina is flexible in moving between billing options. Below are the rules to how transitioning between billing options works:

iCredits Billing Options

New Customers

• Automatically assigned to Post-Paid billing.

• To switch to Pre-Funded billing, purchase Pre-Paid or contract Open Purchase Order iCredits before using Illumina software.

• Any usage before Pre-Funded iCredits are purchased/contracted and registered will be Post-Paid billed.

Existing Customers

• Automatically move to Post-Paid billing if Pre-Funded iCredits are depleted.

• Can move back to Pre-Funded billing by make another purchase or contract.

Samples Billing

• Available only through Pre-Funded billing.

• New and existing customers must purchase Pre-Paid Samples in order to use Illumina software products that consume Samples.

Notifications & Alerts

Illumina provides a range of automated notifications to help users effectively manage their usage and billing, focusing on low balances, threshold alerts, and invoice triggers.

Usage Explorer Usage Notifications

• iCredit Monthly Budget Alerts: Notifications are sent when your configured monthly budget threshold is reached, allowing you to monitor spending and take action before exceeding your planned usage. You can set up or adjust your monthly budget notification at any time in Usage Explorer.

iCredit Pre-Funded Billing Notifications

• Low Balance Alerts: Notifications are sent when both Pre-Paid and contracted Open Purchase Order iCredit balances are low.

iCredit Post-Funded Billing Notifications

• End of Billing Period Alerts: Invoices are sent at the end of each billing cycle.

Sample Post-Funded Billing Notifications

• Sample notifications are planned for release in the upcoming year.

This system ensures users can stay informed and proactive in managing their financial commitments efficiently.

How to avoid unintended charges

Before Your Subscription Expires:

• Review active resources (workflows, pipelines, jobs) and stop anything you no longer need.

• Delete storage and any temporary data you don’t want to keep.

• Download or export anything you need to retain off‑platform.

After Your Subscription Expires:

• Billing for any remaining usage (e.g., stored data you did not delete) continues according to your billing option.

• If your subscription is expired and you cannot access the product to delete storage or shut down usage, contact Support/Customer Care using the contact information at the bottom of this page. We will help restore access so you can remove data and prevent further charges.

Best Practices to Avoid Unwanted Charges

• Set alerts in Usage Explorer.

• Schedule a pre‑expiry cleanup: shut down jobs and delete storage you don’t need.

• Use project tags/labels to find and remove old or orphaned resources quickly.

• Review Usage Explorer weekly to catch unexpected activity.

Summary

• Illumina software usage is billed through: iCredits and Samples.

• iCredits support post-paid (monthly invoicing) or pre-funded billing.

• Samples are pre-funded only.

• If pre-funded iCredits are depleted, billing switches to post-paid automatically.

• Use Usage Explorer to monitor usage, balances, and forecast spend.

Help and Support

For customer service inquiries, email: [email protected]

Visit our website at: www.illumina.com

The allocated quantity is used up, or

The Sample purchase appears as a prepaid transaction (not as post‑paid usage).

Configure Cloud Connectivity in NextSeq Control Software

1. From the NextSeq Control Software home page, navigate to Manage Instrument.

2. Select System Configuration.

3. Select BaseSpace Sequence Hub Configuration.

4. Change the Hosting Location to the appropriate region and check the box for Private Domain. Enter your domain name in the text box to designate the Enterprise Account Domain. Then select Save.

Configure BaseSpace

1. Log in to BaseSpace as the Workgroup Owner and make sure the desired workgroup is selected.

Workgroup Administrators can change the workgroup owner in IAM Console

1. Click on the workgroup name from the BaseSpace header, select Settings from the expanded menu.

2. Make sure ICA Run Storage is turned on.

Configure Connected Insights

1. Log in and navigate to Connected Insights, making sure the same workgroup is selected as in the previous steps.

2. Optional: Navigate to Configuration -> Report Automation and configure report automation with preferred settings. This feature allows for the automatic generation of a draft report based on user settings.

1. Navigate to Configuration -> Test Definition and create a test definition with GRCh37 human reference genome. Turn on Report Automation if you configured report automation settings in the previous step.

1. Navigate to Configuration -> Data Upload -> From Illumina Connected Analytics, add the DRAGEN TruSight Oncology 500 Analysis Software v2.5.2 (with HRD) pipeline, and select the test definition created in the previous step.

Plan the Sequencing Run in BaseSpace

1. Log in to BaseSpace and make sure the same workgroup is selected.

2. Navigate to the Runs tab, select New Run, and then select Run Planning.

1. Select Instrument Platform as "NextSeq 500/550".

2. Set the Secondary Analysis to "BaseSpace/Illumina Connected Analytics".

The configuration input forms vary depending on the instrument platform, secondary analysis pipeline, and other selections (see Sequencer Auto-launch Analyses Compatibility for details). The following images demonstrate screens using a NextSeq 550 instrument with DRAGEN TruSight Oncology 500 Analysis Software v2.5.2 (with HRD) analysis.

1. Select "DRAGEN TruSight Oncology 500 Analysis Software - 2.5.2 (with HRD)" from the Application dropdown menu.

2. Select "TruSight Oncology 500" from the Library Prep Kit dropdown menu.

3. Select "TruSight Oncology 500 (NovaSeq6000Dx with SP Flow Cell, NovaSeq6000, NextSeq)" from the Index Adapter Kit dropdown menu.

4. Click Next to continue.

1. Use default values for Index Reads, Read Type, and Read Length or change as needed.

2. Input Sample IDs and appropriate Index IDs for each sample. Alternatively, download a sample template and use it to import the sample information.

3. In Per Sample Configuration, add Sample Type, Pair ID and Sample Feature. One DNA sample and one RNA sample can be paired and analyzed in Connected Insights in a single case if they share the same Pair ID.

4. Upon completion, export sequencing run settings as a SampleSheet.csv file.

Optional: Update the Sample Sheet to Provide Disease Information

Connected Insights requires sample's disease information to start the analysis. Users can provide disease information in several ways, incorporating disease information into the sample sheet is one of them.

1. Use a text editor to open the SampleSheet.csv file generated in the previous step.

1. Find [Cloud_TSO500S_Data] section.

2. Add ,Tumor_Type at the end of the next line after [Cloud_TSO500S_Data].

3. Add SNOMED CT code for each sample following a ,. Note: samples sharing the same Pair ID should have the same Tumor Type.

4. Save the file.

Set Up Sequencing Run with Cloud Analysis Sample Sheet

1. From the NextSeq Control Software Home screen, select Experiment.

2. On the Select Assay screen, select Sequence.

3. On the Run Setup screen, select Manual as run mode.

4. Select Use BaseSpace Sequence Hub Setting and then select "Run Monitoring and Storage". Enter your BaseSpace Sequencing Hub username and password. If prompted, select a workgroup to upload run data to. You are prompted only if you belong to multiple workgroups.

5. Select Next.

6. Enter a run name of your preference.

7. Optional: Enter a library ID of your preference.

8. From the Recipe drop-down list, select a recipe. Only compatible recipes are listed.

9. Select Paired-End as read type.

10. Enter the number of cycles for each read in the sequencing run using the same value as the sample sheet generated from previous step.

11. Set the output folder location for the current run. Select Browse to navigate to a network location.

12. Select Browse to navigate to a sample sheet.

13. Select Purge consumables for this run. The setting purges consumables automatically after the current run.

14. Select Next.

15. Select Next to start the sequencing.

Monitoring Sequencing Run

Sequencing run results will be uploaded to ICA. Users can monitor the sequencing run status from the instrument or BaseSpace.

Secondary Analysis Auto-launch

Secondary analysis will automatically start upon the sequencing run completion. Users can monitor the secondary analysis status from BaseSpace or ICA.

Tertiary Analysis Auto-launch in Connected Insights

Cases are automatically created in Connected Insights upon the successful completion of secondary analysis. The tertiary analysis automatically starts if disease information is provided in the sample sheet.

If disease information was not provided in the sample sheet, the case will be created with the "Missing Required Data" status. To start the analysis, follow these steps:

1. Log in to Connected Insights and make sure the right workgroup is selected.

2. Open a case with the "Missing Required Data" status.

1. Click the Edit Case button, then input the tumor type in the Disease field.

2. Click the Save button. The case will start processing after a few seconds.

For additional options to provide case disease information with the Case Metadata file, access [DATA UPLOAD -> Custom Case Data Upload] in the Connected Insights user guide accessible in the software.

View Tertiary Analysis Results

Users can open the case to review the tertiary analysis results after the case finishes processing and the status changes to "Ready for Interpretation". A draft report will be ready for review if the Report Automation feature is turned on.

Requeue Secondary Analysis

Use the following steps to requeue secondary analysis in case of its failure:

1. Delete failed cases in Connected Insights if needed.

2. Log in to BaseSpace and open the run.

3. Click the hourglass icon, then select Requeue -> Planned Run.

1. Choose either the Sample Sheet from the run or upload a new Sample Sheet to requeue the secondary analysis.

1. New cases will be created in Connected Insights after the secondary analysis completes.

Fixed an issue where the Product Dashboard was not displayed after logging in using the new login experience.

Admin Console

• Removed the low/negative iCredit balance banners in favor of the new "Usage Explorer" view

• Fixed issue preventing registration of BaseSpace Professional subscriptions when users were logged with a user other than their public domain user.