Version 93 Updates

We are happy to introduce several enhancements and new features in our latest update:

Starting April 15 2026, Franklin’s free tier will include a limit of 10 case uploads per organization per month. All case capabilities and features will remain available, including ACMG classification, ClinVar integration, and case management. Importantly, variant search will remain unlimited.

This change will help us continue improving platform performance, reliability, and the features your lab depends on. Organizations that require higher throughput can upgrade to a paid plan. Learn more in the following Help Center article.

A new Roles & Permissions tab is now available from the Settings page. A user role defines the permissions for performing user actions in Franklin, such as Create case, Classify, or Add to Report. The new Roles & Permissions tab enables you to manage your organization’s user roles, including viewing, creation, and editing of user roles. Example of the new Roles & Permissions tab, showing all user roles of an organization:
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Clicking a user role opens a popup that shows how each permission is set for this role (allowed or blocked):

The permissions are grouped into different action types, namely Accession, Classification, Curation & Knowledge Base, and Reporting. An info icon adjacent to a permission name provides an explanatory tooltip on hover.
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Notes:
-Only admin users can create and edit user roles; non-admin users can only view them.
-A “Default role” appears in all organizations. The default role is automatically assigned to a user that does not have another assigned role, e.g. a new user that was invited without a role assigned in the invitation (see Assign User Roles when Inviting Members, below). The permissions of the default role are editable (as in any user role), while its name is not.

Roles & Permission tab is available for Franklin Premium users upon request - to gain access, please contact our support team ([email protected]). For more information on user roles, please visit the following Help Center article.

The Members table, found in Organizational Info tab of the Settings page, is now located in a dedicated Members tab. Admins can now assign user roles to members when user roles are enabled for the organization. A user role field is available in the Members table to the left of the organizational role field (Admin/Member), allowing for easy selection of a single role per user:
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A user role field is now also available in the Invite Team Member popup, enabling to assign a role which will be applied once the invited team member has joined. The default role is selected automatically, and a different role can be selected instead:
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Note that the Invite Teammates option in Franklin’s main menu now redirects to the Members tab. User role assignment is available for Franklin Premium users upon request - to gain access, please contact our support team ([email protected]). For more information on user roles, please visit the following Help Center article.

The Assays page is now available for all Franklin Premium users. It is available from Assets > Assays in Franklin’s main menu:

View All Assays leads to a page that shows all of your organization assays:

Clicking an assay tile opens the assay page, which displays key information pertaining to the assay’s bioinformatic pipeline, Workbench configuration including filters, Variants page filters, and the Report export format. Only germline assays are presently supported (including hereditary cancer). An assay’s page Edit Assay button, available for admin users, presently allows editing the Workbench configuration - opting-in/out to Franklin’s default Workbench variants, applying filtering by priority, and setting quick filters (Variants page filters) as Workbench inclusion or exclusion filters:

Saving changes when editing the Workbench configuration will have an effect on new cases, i.e. cases created after the assay has been edited. It will also affect an existing case in its next Workbench recalculation; recalculation occurs when phenotypes or soft panels are added or removed, or if the case is reanalyzed. For more information on Assays page, please visit the following Help Center article.

The HGMD version is now displayed in the top-right corner of the HGMD widget in both the Variant Assessment and Gene Assessment tabs. In the Gene Assessment tab, the HGMD mutation transcript is also available in the Gene Mutations table within the HGMD widget.

Similar to Cases view in All Cases, Batch view now supports bulk actions - selecting multiple specific cases within a batch or across batches, and performing actions on these cases. The available actions are change status, assign to user, and apply labels. The number of selected cases is displayed by a counter within the batch tile, as well as by a global counter that also shows the number of batches in which cases are selected.

This enhancement decreases the time required for performing key actions on multiple cases when viewing cases as batches. For more information on Batch View, please visit the following Help Center article.

Similar to germline cases, the Case Details tab is now available in tumor (somatic) cases, with case comments, protocols, patient and sample details, hard and soft panels, and additional details available. The Sample Information section shows somatic fields, including cancer type, tumor purity, and tissue type, as well as custom fields:

Additionally, all available sample files can be downloaded directly in this tab.

In tumor (somatic) cases, fusion variant tiles now display a single location icon, similar to other variant types. Clicking the location icon or the adjacent location text lets you open the fusion in desktop IGV or browser IGV, as was available until now only from Variant Assessment tab in the variant popup. Clicking the location icon additionally allows you to copy the breakpoint genomic coordinates to clipboard in the format “<5’ breakpoint chr>:<5’ breakpoint position>::<3’ breakpoint chr>:<3’ breakpoint position>”, for example “chr17:48271304::chr22:39631879”, making it easier to view and share precise breakpoint location information.

In addition, the breakpoint genomic location displayed in the fusion variant popup header is now displayed using the same format.

In tumor (somatic) cases, fusion variants can now be manually added to the case from the Workbench’s “Add variant” link, similar to adding SNP or CNV variants.

You can add fusions by entering genomic breakpoint locations in the format “Fusion:<5’ breakpoint chr>:<5’ breakpoint position>::<3’ breakpoint chr>:<3’ breakpoint position>”, for example “Fusion:ch22:23660224::chr9:133589333”, as shown in the Fusion example button. Adding fusions is available in DNA-only, RNA-only, or DNA+RNA tumor cases; manually added fusions will be annotated as RNA fusions and displayed on the Workbench with an indicative tile comment. Added fusions can be classified and added to the Report. This enhancement allows adding fusions from runs, sources, or methods that are external to the case.

When working with somatic cases that include both RNA and DNA data, you can now view RNA variants and fusion variants in Desktop IGV using the RNA BAM file, and view SNP and CNV using the DNA BAM file. The "Open with desktop IGV" option from a variant tile or Variant Assessment tab will automatically select the correct BAM file based on the variant type. Selecting "Open with desktop IGV" from the case menu will continue to use the DNA BAM. RNA-only and DNA-only case behaviors are unchanged. This streamlined handling enables seamless visualization of both RNA and DNA evidence.

Custom reference genome FASTA file for viewing variants in Desktop IGV can now be configured in a germline or somatic assay. Separate FASTA files can be configured for DNA and RNA variants (including fusions). A custom locus can be used for RNA variants in somatic assays, where ID information from a VCF is passed to desktop IGV, supporting RNA variant display from e.g. Ion Torrent somatic workflows. To configure a custom reference genome or locus for your assay, contact our support team ([email protected]).

The Organization Name field on the Organization Info section of Settings page is now editable using an Edit button instead of by text editing as previously available. The edit button is available for admin users only.

Resolved an issue where a tree compound label configured as a Workbench filter generates an error in the Workbench and Variants page.

Resolved an issue where searching the Members table in the Settings page (now included in a dedicated Members section) returns empty results on repeated searches.