Final compute cost is now displayed for analyses that execute in ICA.
Added the ability to delete an analysis when data is partially owned by another user (i.e., following a project transfer). Only data owned by the user will be deleted, and other users with analysis data will retain access to the analysis details.
Updated the file preview modal to include a link to the analysis files tab. The link appears when viewing a file without the analysis context, such as in search results.
Added a note on the Microarray Analysis Setup sample selection page to indicate when a sample sheet with additional information is recommended for the selected analysis.
Added an info icon with an explanatory tooltip when a run's data status is 'Zipped' or 'Zipping'.
Bugs Fixed
Fixed an issue that could cause an analysis details page to get stuck while loading.
Fixed an issue that could result in an error when attempting to empty the trash or restore items.
Fixed an issue that could cause 'analysis completed' emails to be erroneously sent immediately after launching certain apps.
7.5.0 - Performance Enhancements
October 18, 2022
Features
Improved allocation of compute resources leading to decreased app startup times.
Improved performance of the 'get project' CLI command when filtering on project name.
Bugs Fixed
Fixed an issue in Run Planning where white space before or after the Run Name could cause a validation error on the instrument.
Improved the behavior when viewing files in the search feature. Clicking a file name will now open the file preview modal, allowing the file to be viewed and/or downloaded.
Clarified the different options available when moving runs and datasets to the trash.
Security updates and fixes.
Bugs Fixed
Fixed an issue that could cause some files to be retained following the deletion of a run.
Fixed an issue that occurred after updating the owner of a workgroup that continued to charge the original owner's storage to the workgroup.
Fixed an issue that allowed a project to be transferred when it contained analyses in statuses that are not eligible for transfer (e.g., running).
Added the ability to delete custom library prep kits and index adapter kits from the Resources page.
Bugs Fixed
Fixed an issue that prevented the transfer of projects containing NextSeq 1000/2000 and BCL Convert analysis data. Staged Rollout.
Fixed an issue that could cause a NovaSeq X Local mode run to be incorrectly stuck in the Uploading status.
Fixed an issue when transferring Projects that could prevent associated Biosamples from showing up for the recipient.
Release 7.18.1 - February 12, 2024
Features
None.
Bugs Fixed
7.40.0 - BaseSpace Downloader 3.1
November 18, 2025
Features
Adapter Read 1 and 2 can now be edited during run setup for easier customisation.
Bugs Fixed
Fixed an issue that prevented downloads when system certificates could not be verified.
Fixed an issue that could cause an 'Apple could not verify' warning to appear when installing the BaseSpace Downloader on Mac.
Downloader UI improvements and fixes.
Known Issues
The copy and merge features are currently unavailable for samples generated by BCL Convert.
7.42.0 - BaseSpace CLI 1.7.0
January 20, 2026
Features
7.33.0 - Shared BCL Convert Section
April 23, 2025
Features
7.13.0 - Sharing for NovaSeq X Runs and Analyses
June 20th, 2023
Features
7.7.0 - NovaSeqX Support
December 13, 2022
Features
7.25.0 - Project Column in the Analysis Files Tab
August 20, 2024
Features
7.38.0 - App Deprecations
September 16, 2025
Features
7.9.0 - Multi-Analysis Run Planning
February 14th, 2023
Features
7.41.0 - Run Planning Improvements
December 16, 2025
Features
7.10.0 - NovaSeq X Analysis Autolaunch Improvements
March 21st, 2023
Features
7.17.0 - Deletion of Biosample Default Projects
Dec 19th, 2023
Features
Previous Releases
⬅️ Navigate the tree in the left-column to explore previous releases of Basespace Sequence Hub.
7.4.0 - Run Planning Enhancements
September 21, 2022
Features
7.16.0 - Transfer of NovaSeq X Runs
Oct 17th, 2023
Features
7.31.0 - Usage Explorer
February 18, 2025
Features
Fixed an issue that could cause run and project transfers to become stuck.
Fixed a rare issue where an App launch could result in two analyses.
A new version of the BaseSpace Downloader for Windows has been made available, that fixes network connection issues experienced by some users. A security warning about untrusted software may be shown during installation.
Fixed an issue that could update lane-library mappings when analysis completes on a shared run.
Fixed an issue that could prevent the Analysis Inputs tab from loading.
Updated the BaseSpace CLI to version 1.7.0. Download the latest version and see the release notes here.
Improved error messages returned by sample sheet validation during Requeue Analysis, Library QC App launch, and Import Run.
Allow Dataset file to be imported as Reference File for Run Planning
Improve performance of project list.
Bugs Fixed
Fixed native app cost discrepancy between BaseSpace and UPA.
More reliable indexing of output files from analyses that are automatically transitioned to "timed out" status.
Set standard input properties on ICA analyses, improving behavior in context of automated workflows.
Downloader 3.2
Properly sanitize filenames containing characters not supported by the user's operating system.
Multiple UI improvements and bugfixes
Known Issues
The copy and merge features are currently unavailable for samples generated by BCL Convert.
Updated Run Planning to display a "Shared BCL Convert" section for platforms supporting multiple analysis configurations. The section shows on the Run Review page and displays the BCL Convert version and the settings that will be used.
Added notifications in Run Planning when changes to the planned run affect the version or settings of the shared BCL Convert configuration.
Added support to import settings from an Analysis Configuration Template directly into Run Planning.
Combined the Pillar ONCO/Reveal™ library prep kits into a single Pillar oncoReveal™ kit, and added three new compatible index adapter kits.
Clicking a file on the Analysis Inputs tab now opens the file preview modal, allowing the file to be viewed and/or downloaded.
Bugs Fixed
Improved the process of timing out analyses that become stuck during post-processing.
Fixed an issue on the Analysis details page that would incorrectly display a compute charge of 0 iCredits for certain applications. This issue was in the display only and did not affect billing.
Fixed an issue in the CLI where an error message would not list the correct scopes required.
Fixed an issue in storage-related emails where the storage limit unit (TB) was not displayed.
Release 7.33.1 - April 28, 2025
Features
None.
Bugs Fixed
Stability and performance improvements.
Added support for sharing NovaSeq X Runs and autolaunched Analyses.
Added the option to upload a new sample sheet when requeueing from a planned run.
Added the ability to archive runs in "Needs Attention" status.
Updated the look and feel of the Analysis list and the Analysis Files tab.
Native App engine update - Staged roll out.
Improved error handling and performance.
Bugs Fixed
Fixed a confusing error message when uploading a NovaSeqX manual mode run without a sample sheet.
Fixed an issue that caused CLI uploads to incorrectly display "Report is still being generated" on the Reports tab.
Fixed an issue where a new biosample could not be created when uploading FASTQ files to a Project.
Fixed an issue where a read 2 FASTQ file uploaded without a corresponding read 1 file wouldn't cause a warning.
Fixed an issue when requeueing a planned run where the Lane Usage checkbox could be incorrectly unchecked.
Fixed an issue that could cause certain apps to get stuck in Running.
Fixed an issue on the Search page where a long search term runs off screen.
Known Issues
Starting in August, uploads from instruments running Windows versions 7 or earlier will no longer be supported.
After uploading files, BaseSpace displays a blank analysis page. Reload the page to see upload information and files.
Added support for NovaSeqX and NovaSeqX Plus instrument types.
Bugs Fixed
Fixed an issue that could prevent biosample yield from appearing after BCL Convert completes.
Fixed an issue that could cause analyses to hang in the "Running" state.
Fixed an issue that could cause restoration of archived files to fail.
When creating a custom kit during run planning, the newly created prep kit will now be auto-selected.
Release 7.7.1 - December 19th, 2022
Features
None.
Bugs Fixed
Fixed an issue that could prevent analyses from transitioning to the 'Complete' state.
Fixed an issue that could prevent linking of FASTQ Datasets upon completion of DRAGEN FASTQ Toolkit.
Updated the Analysis Files tab to include a project column with the associated output project.
Runs will now transition to the "Timed Out" status if they have not completed 14 days after upload starts, or 8 days after secondary analysis starts.
Reordered the items in the Status > Requeue menu.
Deprecated NeoPrep functionality.
Minor UI updates and fixes.
Bugs Fixed
Fixed an issue that could prevent the sample sheet from loading on the Requeue Sample Sheet page when a custom sample sheet name was used.
Fixed an issue that could prevent requeueing runs that were uploaded without an initial sample sheet.
Fixed an issue where BCL Convert 2.5.0 was not updating the run status upon completion.
Fixed an issue that prevented unzipping a zipped run when the run folder contained a Logs.zip file.
Release 7.25.1 - August 29, 2024
Features
None.
Bugs Fixed
Fixed an issue that could cause the Analysis Reports tab to display a blank space instead of a report.
Stability and performance improvements.
We are deprecating a significant number of applications on BaseSpace. See Release Notifications for more information.
Updated Run Planning so that Adapter sequence reads are always displayed regardless of the instrument type.
Clarified the allowable values for the redirect URI field in the Developer Portal.
Bugs Fixed
Fixed an issue that could cause a run or project transfer to become stuck.
Improved the message for a permissions error that can occur when launching an app.
Known Issues
The copy and merge features are currently unavailable for samples generated by BCL Convert.
BaseSpace Ground Control 2.31.1 - October 9, 2025
Features
None.
Bugs Fixed
Fixed an error that could occur during BaseSpace login on sequencing instruments.
Added additional support for NovaSeqX instruments.
Improved integration for datasets, biosamples, reports, and metrics generated by analyses run in ICA.
Moved the Run Planning pages for viewing and creating kits, genomes, and reference files out of Settings and into a new Resources page. This page can be accessed through the Account drop-down list, by clicking "Resources".
Run Planning additions and improvements:
Added the ability to configure multiple secondary analysis configurations, for supported instrument types.
Added a "fill down" function for the Lane column in the Sample Table. Doing so will copy the first row's value to all other rows.
Bugs Fixed
Improved the performance of pages displaying large tables and lists.
Fixed a bug in Run Planning where error messages would refer to Well Position instead of Index ID.
Release 7.9.1 - February 20th, 2023
Features
None.
Bugs Fixed
Fixed an issue that could cause BCL Convert appsessions to stall during post-processing in cases where a sample was sequenced across multiple lanes.
Fixed an issue that caused reports from certain apps to fail to load for completed analyses.
Known Issues
When multiple datasets with the same name are generated from an analysis, only one for each name is displayed on the Analysis Files tab.
Enhanced Run Planning to display warnings, e.g. for deprecated apps
Updated "Local" Analysis Location label in Run Planning to "On Instrument (Local)"
Enhanced Run Planning to retain BCL Convert per-sample settings imported from sample sheet
Improved performance of deletes with large number of items
Better cleanup of background processes preventing project transfer
Bugs Fixed
Fix login from certain instruments where user needs to accept agreements
Prevent users from seeing and deleting hidden analyses
Fixed issue where QC recalculation could fail if appsession wasn’t complete, causing downstream workflows to misfire. QC update now occurs only after appsession completion to ensure correct status transitions.
Improved billing for some older apps
Security and performance fixes
Known Issues
The copy and merge features are currently unavailable for samples generated by BCL Convert.
Improved error logging for NovaSeq X autolaunched analyses.
Improved the sample sheet viewer in the Analysis Inputs tab for apps that use a run or sample sheet as input.
Added Lane Usage checkbox in Run Planning's Configuration page, as an alternative way to configure for the use case where samples are loaded across all lanes. When this option is enabled, lane column will not be included in the sample sheet.
Added filter support in Application, Library Prep Kit, Index Adapter Kit, and Reference Genome dropdown fields in Run Planning
Bugs Fixed
Fixed an issue where certain paid apps could be launched regardless of subscription status or iCredit balance.
Fixed an issue that could cause BCL Convert analyses to complete before Biosample yield was finalized. Note that this fix may cause slightly longer analysis durations due to increased post-processing time, but billing will only be for the analysis running time.
Fixed an issue that could cause a status summary message of "in progress" to appear for a completed analysis.
Fixed an issue that could incorrectly transition the status of a run from Needs Attention to Complete.
Fixed an issue where an invalid combination of standard Library Prep Kit Index and Not Specified Adapter Kit is allowed in Run Planning
Fixed an issue that could cause sample sheets with custom names to be ignored when uploaded using the CLI.
Fixed an issue in the list files API that could cause sort parameters to be ignored.
Added support for deleting Projects that are Biosample default projects. Deleting or transferring a default project will remove the association from all related Biosamples. Staged rollout complete January 4 2024.
Improved performance of moving data to the trash:
Moving a project to the trash is now an asyncronous operation.
Added a "Trash Status" column to items in the trash. The percentage indicates how much of the data has been moved into the trash.
Added support for FASTQ Dataset copy when the source FASTQ file is in ICA Storage.
Updated the 'Analysis Has Succeeded' email to include a warning if any nodes were unsuccessful.
Updated the pricing and cost for apps that run on ICA to link to the iCredit pricing page.
When using Run Planning to requeue an analysis, uploading a sample sheet now has the option to skip validations and submit as-is.
Added support in Run Planning for uploading reference files directly from the analysis configuration page.
Bugs Fixed
Fixed a rare issue that could incorrectly charge compute for a timed-out analysis.
Fixed an issue that could cause NextSeq 1000/2000 autolaunched analysis to fail shortly after launching.
Improved the error message when sharing or transferring a project or run containing archived files.
Fixed an issue where Run Planning could not load a NextSeq 1000/2000 planned run created in Clarity LIMS.
Fixed an issue in Run Planning that could prevent the configuration page from displaying properly.
Fixed an issue in Run Planning that could cause a selected reference genome to carry over when creating a new configuration.
Fixed an issue in Run Planning that occured when switching from a standard kit to 'Not Specified'.
Fixed an issue in Run Planning where Local analysis planned runs with periods in the run name would not download.
Run Planning:
Renamed "Instrument Run Setup" to "Run Planning" in the New Run dropdown menu.
Run planning now consists of three stages: run settings, analysis configurations, and run review.
Added a "Save as Draft" option when planning a run. Draft runs are available through Sequence Hub but not on instruments. Once a draft is saved as Planned, it is available on supported instruments.
Improved the ability to import samples from a CSV file. A template CSV is provided for download, and v2 Sample Sheets can still be used to import samples.
Added multi-selection support for the Lane column in the Sample table.
Added new optional fields under run settings: Run Description and Library Tube ID.
Note that there is no change to saved data. Planned runs created using the previous version can still be viewed in Run Planning.
Removed product filter from Beadchip selection table in the Microarray Analysis Setup tool
Bugs Fixed
Improved error messages when launching an app with the API or CLI and no valid FASTQ files are found.
Improved performance when retrieving biosamples in preptab.
Fixed an issue that could cause the email notification checkboxes in Settings to be unchecked even when turned on.
Added the ability to transfer NovaSeq X runs and runs that have been uploaded to ICA Storage.
When creating or editing a reference file for run planning, the compatible DRAGEN versions are displayed next to each genome option.
Uploading a reference file now shows a progress bar and gives the ability to cancel the upload.
Improved emptying the trash to be more robust.
Updated the DELETE v2/trash endpoint to return a 409 when a previous delete request is still in progress.
Added two new fields to items returned by the GET v2/trash response, TrashStatus and CompletedChildEvents.
Bugs Fixed
Fixed an issue that could prevent logs and other output files from being returned when an autolaunched analysis did not complete successfully.
Fixed an issue where FASTQ Datasets were not being created for unindexed reads after running BCL Convert.
Fixed an issue that prevented requeue of NovaSeq X manual mode runs.
Fixed an issue that could cause requeued NovaSeq X analyses to fail.
Fixed a rare issue that could lead to incorrect billing when an analysis times out.
Fixed an issue that affected certain analyses where the "Ica Workflow Session Id" was incorrectly referred to as the "Ica Analysis Id" in the analysis log.
Fixed an issue in Microarray Analysis Setup where threshold values were being reset after selecting a project.
Fixed an issue in Microarray Analysis Setup where only the latest analysis version of an analysis was selectable.
Fixed an issue in Run Planning where a duplicate Index ID error was not clearing after resolving the issue.
Fixed an issue when creating a custom Library Prep Kit that prevented the Compatible Index Adapter Kits dropdown from displaying correctly.
Fixed an issue in Run Planning that could prevent the addition of new configurations before the limit was reached.
Release 7.16.1 - November 9th, 2023
Features
None.
Bugs Fixed
Native App Engine update - stability and performance improvements.
Release 7.16.2 - December 4th, 2023
Features
None.
Bugs Fixed
Stability and performance improvements.
Combined the Usage and Storage tabs into a single tab on the Settings page.
Removed the usage table and added a link to the new Usage Explorer tool.
Storage now shows a single chart with the proportion of data across Runs, Projects, and Trash. Shared data is no longer displayed.
Updated the terms and conditions. The new agreement must be accepted before browsing the BaseSpace website.
Improved the look and feel of the Terms of Service page.
Runs in 'Needs Attention' status can now be renamed and transferred.
Added a project link to the Analysis Reports and Analysis Inputs tabs.
Added a checkbox in Run Planning to use samples across all lanes, removing the need to set lane numbers.
Bugs Fixed
Fixed a rare issue that could create duplicate biosamples when running sides A and B simultaneously on NovaSeq X instruments.
Fixed an issue that could cause analysis autolaunch to fail after uploading the run with a CLI version older than 1.5.2.
Fixed an issue that allowed certain analyses to be aborted during post-processing.
Fixed an issue in Run Planning that prevented the Sample Table columns from updating correctly when changing kit selection from a standard or custom kit to "Not Specified".
Fixed an issue that prevented setting the custom reference file field when creating an Analysis Configuration Template for the DRAGEN Microbial Enrichment application.
Fixed an issue that prevented error messages from displaying on the Archive dialog box.
Projects, datasets, and analyses with files stored in ICA can now be moved to the trash and deleted.
Bugs Fixed
Fixed an issue with the Instrument Run Setup tool, where the Lane column was incorrectly validated when using “Not Specified” for library prep kit.
Fixed an issue that could incorrectly set the size of an Analysis to 0.
Fixed an issue on the Run Sample Sheet tab where Date field values were incorrectly formatted.
Known Issues
FASTQ Generation and other apps very infrequently abort while uploading results.
For customers using Instrument Run Set up to create a v2 sample sheet for a NovaSeq SP 500 cycle run, the sample sheet produced has the I5 index sequence in the incorrect orientation. This assigns all sample reads to undetermined. To correct the issue, we recommend removing the "IndexOrientation Forward" flag from the [Header] section of the sample sheet.
Release 6.19.1 - March 31, 2022
Bugs Fixed
Fixed an issue in the application editing page used by administrators.
7.0.0 - Datasets and Apps Performance
April 19, 2022
Features
Improved the performance and stability of the datasets API.
Native App engine update - Staged roll out.
Improved error handing and performance.
Fixed an issue where FASTQ Generation and other apps could fail while uploading results.
Bugs Fixed
Fixed an issue that could cause an error when using the CLI to launch an application with a multi-select field.
Fixed an issue in the library prep kit TSV template where the Adapter Read 2 value was not imported correctly.
7.12.0 - Combined New and Classic Modes
May 17th, 2023
Features
Combined New and Classic modes into a single view.
Removed the New/Classic application switch from Settings.
Allow Biosample/Sample selection from the app launch pages.
Run and Project pages now display both Biosample and Sample tabs.
Updated the look and feel of the Project list, Project details, file upload, trash, and search pages.
Improved error messages when importing samples into the Run Planning tool.
The Usage page in Settings now includes a link to the Admin Console for domain admins.
Added support for IDAT file upload in Microarray Analysis Planning.
Bugs Fixed
Fixed an issue that could cause NovaSeq X auto-launched analyses to get stuck in "Running".
Fixed an issue where 'Created' and 'Updated' columns were using incorrect date formats.
Fixed an issue that could cause biosample workflow uploads to launch duplicate analyses.
Known Issues
The following operations cannot be performed for NovaSeq X sequencing runs or analysis results: share, transfer, archive, and editing the run name.
Starting in August, uploads from instruments running Windows versions 7 or earlier will no longer be supported.
The Lane Usage toggle in Run Planning is not displayed when planning a run on NovaSeq X.
Release 7.12.1 - May 23rd, 2023
Features
None.
Bugs Fixed
7.15.0 - Compatibility Filtering in Run Planning
Sept 19th, 2023
Features
Added application version filtering in Run Planning. For instruments that support multiple analysis configurations, selecting an initial application will filter subsequent configuration application options to ensure compatibility with the BCL Convert version used.
Analyses auto-launched after NovaSeq 6000 and NextSeq 500/550 runs are uploaded to ICA storage will be placed in a folder named "ilmn-analyses" within the ICA project.
Analyses auto-launched after uploading a NovaSeq X run using the CLI will be placed in a folder named "ilmn-analyses" within the ICA project.
Added a link on the Analysis Files tab to the corresponding Analysis in ICA, when applicable. This link appears for users with an active ICA subscription.
Added support for persisting selections across pages in data tables.
AppSessions running longer than 1 week have been manually timed out. This will not result in any iCredit charges.
Bugs Fixed
Fixed an issue when launching the Illumina Complete Long Reads (ICLR) app from the CLI. To use files when launching ICLR, upgrade to the CLI version 1.5.4 or later .
Fixed an issue that could set a Run to Needs Attention status when more than one 'SampleSheet.csv' files are present in the run folder.
Fixed an issue that could occur during CLI upload of a Run folder where the --sample-sheet parameter is ignored.
Release 7.15.1 - Sept 25, 2023
Features
None.
Bugs Fixed
7.27.0 - App Store Upgrade
October 15, 2024
Features
Updated the look and feel of the Apps page.
Added a "Status" column in Analysis Files page to display archive status.
Updated the Project list page to make columns resizable.
Added the ability to cancel auto-launched or re-queued v2 sample sheet analyses.
Made improvements to the Microarray Data Management upload date range filter.
Added more detailed progress bar during Microarray Data Management data deletion process.
Added column filter for Run Planning Sample table.
Added the ability to view and edit custom kits in the Resources > Index Adapter Kits page.
Bugs Fixed
Fixed an issue that could cause analyses to get stuck in the Initializing status.
Fixed an issue that made Indexing QC information unavailable for multi-node FASTQ Generation analyses.
Fixed an issue where the cancel button was still enabled while deleting microarray data.
7.22.0 - Analysis Autolaunch for NovaSeq X Manual Mode Runs
May 21, 2024
Features
Added analysis autolaunch support for NovaSeq X manual mode runs with a sample sheet.
Added the option to switch to the correct Workgroup when following a Biosample link.
Minor UI updates and fixes.
Bugs Fixed
Fixed an issue that could cause an incorrect version of native FASTQ Generation to be launched on run upload.
Fixed an issue that could cause an analysis to continue running after moving the project to the trash.
Fixed an issue that could cause a requeue with a new sample sheet to fail.
Release 7.22.1 - May 29, 2024
Features
None.
Bugs Fixed
7.23.0 - BaseSpace CLI v1.6.0
June 20, 2024
Features
Updated the BaseSpace CLI to version 1.6.0. Download the lastest version and see the release notes .
Minor UI updates to the action toolbar dropdown menus.
Bugs Fixed
Security improvements and fixes.
Fixed an issue that prevented screenshots from displaying correctly on Application details pages.
Fixed an issue that prevented PDFs from displaying properly when previewing from a file browser.
6.17.0 - Preliminary ICA Integration
January 27, 2022
Features
Added support for Illumina Connected Analytics (ICA v2) integration. Staged rollout.
Bugs Fixed
Fixed an issue in Microarray Analysis Setup where previously entered values were not cleared when switching user context.
Increased reliability of automated customer e-mails.
Release 6.17.1 - January 31, 2022
Bugs Fixed
Improved stability of ICA integration across regions.
Release 6.17.2 February 4, 2022
Bugs Fixed
Updated the Native App Engine to fix an issue where interrupted system calls can produce errors in FASTQ Generation.
Known Issues
7.3.0 - Improve App Launch Performance
August 16, 2022
Features
Improved performance of app launch when using more than three Biosamples. Certain validations will now be performed during initialization and any errors will be displayed in the analysis log.
Improved performance of the v2/datasets API.
Bugs Fixed
Fixed an issue that prevented unlocking a Biosample using the status menu.
Fixed a rare issue that could affect datasets from multi-project analyses when one of the projects is deleted.
Fixed an issue causing the action buttons on the Biosample matcher modal to run off screen.
Known Issues
Occasional delays in search indexing can result in Biosamples not appearing immediately after creation.
Release 7.3.1 - August 24th, 2022
Features
None.
Bugs Fixed
Release 7.3.2 - September 12th, 2022
Features
None.
Bugs Fixed
7.11.0 - NovaSeq X Analysis Requeue
April 18th, 2023
Features
Added the ability to requeue runs using the Run Planning tool. Currently supports requeue of analyses from Illumina DRAGEN Apps v4.1 and higher and DRAGEN TruSight Oncology 500 Apps 2.1 and higher. Staged rollout.
Added two new applications categories to the App Store: Illumina and Dragen. The App Store now filters for the Dragen category by default.
Renamed the application category "Synthetic Long Reads" to "Long Reads".
Improved the performance of post-processing analysis results from NovaSeq X.
Added copyright information to each page.
Bugs Fixed
Fixed an issue that prevented download of NovaSeq X runs using the BaseSpace CLI.
Fixed an issue that could cause the Analysis Inputs tab to not load for NovaSeq X autolaunched analyses.
Fixed an issue that could affect deletion of analysis data generated from a NovaSeq X auto-launched app.
Known Issues
The following operations cannot be performed for NovaSeq X sequencing runs or analysis results: share, transfer, archive, and editing the run name.
Beginning with BSSH v7.12.0, uploads from instruments running Windows versions 7 or earlier will no longer be supported.
The Lane Usage toggle in Run Planning is not displayed when planning a run on NovaSeq X.
7.1.0 - FastQ Related Fixes and Performance Improvements
May 18, 2022
Features
Improved performance of biosample creation following the completion of run upload.
Improved performance of QC failing existing FASTQ datasets when re-running BCL Convert.
Added support for updating the default project on biosamples generated by the BCL Convert for ICA app.
Added support for renaming biosamples generated by the BCL Convert for ICA app.
Bugs Fixed
Fixed an issue that could cause BCL Convert to fail when retrieving the number of flow cell lanes.
Fixed an issue that caused deleted FASTQ datasets to remain visible on the Run Biosamples page.
Fixed an issue that could cause apps to fail when selecting large numbers of datasets as input.
Release 7.1.1 - May 19, 2022
Features
None.
Bugs Fixed
Release 7.1.2 - June 22, 2022
Features
None.
Bugs Fixed
7.30.0 - Prep Tab Deprecation
January 21, 2025
Features
Prep functionality is officially deprecated. All run planning and sequencer integration is available through the Run Planning tool.
Added the ability to export a Sample Sheet from the Run Planning Review page when the secondary analysis location is set to BaseSpace.
Improved performance when moving large projects to the trash.
Increased the size of the file preview modal.
Bugs Fixed
Fixed an issue that could cause biosample workflows to time out during post-processing.
Fixed an issue that caused analysis post-processing to fail when a dataset name was too long.
Fixed an issue that prevented errors from displaying in Run Planning when using the Import Samples feature.
7.34.0 - Deletion of Custom Reference Genomes
May 20, 2025
Features
Added the ability to delete custom reference genomes from the Genomes page in the Resources section.
Added 'Archiving' and 'Unarchiving' file statuses for runs and datasets in the process of being archived or restored.
Bugs Fixed
Security fixes.
Fixed an issue that prevented the creation of samples following completion of BCL Convert 4.3.13.
Fixed an issue that caused analysis post-processing to fail when a sample sheet contained the same project name multiple times with different casings.
When uploading FASTQ files, no warning is shown when an R2 file is uploaded without a corresponding R1 file.
When uploading FASTQs, the biosample chooser does not display the option to create a new biosample.
BCL Convert does not generate Samples. To use FASTQ data from BCL Convert, use Biosamples.
Fixed a bug where radio buttons could become disabled on application input forms.
Fixed an issue on the run share dialog that incorrectly suggested runs could be shared with write access.
Fixed an issue in the Run Planning tool where trailing spaces in Run Name were not trimmed on saving.
Fixed issue in Microarray Analysis Setup where any click in the custom filter dropdown would reset the position of the dropdown on scroll/resize.
Fixed an issue in Microarray Analysis Setup where importing too many IDATs resulted in samples not appearing ready for analysis.
Fixed an issue in the Microarray Data Management table where dates remained visible in the calendar view after clearing filter.
Fixed a typo in the Archive and Restore dialogue boxes.
Fixed an issue that prevented the number on the trash icon from updating when switching workgroups.
Fixed an issue that could prevent scrolling after switching workgroups.
Fixed an issue with the Archive Restore modal where the "Restore Data" button stayed enabled when an error occurred.
Fixed an issue in Run Planning where reference files were not being included when exporting a local run with the DRAGEN v4.2.7 apps.
Fixed an issue in Microarray Analysis Setup where sample sheet import would fail with too many samples.
Fixed an issue that affected sharing, transferring, and downloading of NovaSeq X and NextSeq 1000/2000 runs and analysis data.
Fixed an issue that prevented re-queue of NovaSeqX runs by the new owner after a run was transferred.
Improved behavior when retrieving account subscriptions.
FASTQ Generation and other apps very infrequently abort while uploading results.
Fixed a UI issue where selecting an item would sometimes not change the context of the action menu.
Fixed an issue that affected certain apps when launching them using the BSSH CLI.
Fixed an issue that caused slow loading of available Biosamples in Prep Tab.
Performance and stability fixes.
Fixed an issue that could cause slow app launches when using the CLI or API, occasionally leading to timeouts.
Fixed an issue that could prevent launch of the Reference Builder (Instruments) application.
Fixed an issue in the Run Planning tool where index uniqueness validation is not performed after importing samples from a Sample Sheet.
Fixed a rare issue that could cause FASTQ Generation to launch twice after run upload completes.
Performance and stability fixes.
Security fixes.
Improved the error message when importing sample data in Run Planning from a sample sheet with a different application version that what is currently selected.
Clarified a warning message when downloading FASTQ or SAV files from a run whose BCL files were deleted.
Clarified instructions in the Run Planning custom index adapter kit .tsv template.
Fixed an issue that prevented sharing of a run that had been archived and subsequently files-only deleted.
Fixed an issue in Run Planning that stalled the page after selecting a custom fixed-layout kit containing only a single index.
Updated the analysis size display to only reflect datasets the user has permissions to view.
Bugs Fixed
Fixed an issue that could cause an autolaunched analysis to be marked as complete before all downstream analyses finished.
Fixed an issue that could cause samples produced by the FASTQ Generation app to appear twice in the Analysis Reports tab, and to download duplicate FASTQ files when downloaded.
Fixed an error that could occur when attempting to delete a project using the CLI or API.
Fixed an issue that caused timed out runs to get stuck in 'Pending Analysis' after launching an analysis.
Fixed an issue on the Analysis Reports tab that displayed a summary link when no summary report existed.
Fixed an issue that caused PDF files to immediately download when opening them in a preview window.
Known Issues
The copy and merge features are currently unavailable for samples generated by BCL Convert.
Release 7.36.1 - August 11, 2025
Features
None.
Bugs Fixed
Stability and performance improvements.
Native App Engine update - stability and performance improvements.
Added the ability to unlock multiple biosamples at a time from the biosample list.
Updated the Import Samples feature in Run Planning with "Add" or "Replace" options when importing.
Added a warning message in Run Planning when a Sample ID is reused with different indexes.
Added the ability to specify thresholds for Microarray Analysis Setup Configurations.
Improved samplesheet validations for Microarray Analysis Setup.
Bugs Fixed
Fixed an issue that prevented NovaSeq X Series from showing as an option in the Run Insights tool.
Fixed an issue that could prevent index QC metrics from populating for NovaSeq X runs following BCL Convert analysis.
Fixed an issue that would display a blank Report page after uploading files.
Fixed an issue that could cause Biosamples to get stuck in Sequencing status with no yield.
Fixed an issue that could cause the Analysis Reports tab to be incorrectly enabled or disabled.
Fixed an issue that could result in an error when navigating to the Analysis Reports tab.
Fixed an issue that could enable the Download option for an empty project.
Fixed an issue where attempting to delete a shared appsession redirected to a 403 page rather than displaying an error message.
Fixed an issue that affected the menu actions available on the Project Biosamples tab.
Fixed an issue where filters were missing on FASTQ Dataset lists.
Fixed an issue that could cause a Run to briefly update to Needs Attention after initiating a requeue.
Fixed an issue that prevented showing a warning when a read 2 FASTQ file was uploaded without a corresponding read 1 file.
Fixed an issue that could cause Project transfers to get stuck in a transferring state.
Fixed an issue that could prevent available products from being displayed in the Microarray Analysis Planning tool.
Fixed an issue in Run Planning tool where clearing the selection in the Application field causes the page to freeze.
Fixed an issue in Run Planning tool where the Application + Genome field does not display the selected value.
Fixed an issue where the template could not be downloaded when creating a custom Library Prep Kit for Prep Tab.
Known Issues
When performing certain actions on more than one item (eg, updating FASTQ QC statuses), the dialog box briefly displays before closing on its own when an error is returned.
Release 7.14.1 - August 29th, 2023
Features
None.
Bugs Fixed
Fixed an issue that could cause delays when monitoring runs, loading run charts, and downloading run data.
Fixed an issue that could cause the Project size value to be higher than actual. This only affected the displayed project size; billing remained accurate.
Release 7.14.2 - September 5th, 2023
Features
None.
Bugs Fixed
Performance and stability fixes.
Release 7.14.3 - September 11th, 2023
Features
None.
Bugs Fixed
Performance and stability fixes.
Performance Improvements and Fixes.
Bugs Fixed
Fixed an issue in Run Planning where Next button remains disabled after copy-pasting data into Sample Table.
Fixed an issue in Run Planning where Application name is not displayed when editing a planned run's configuration.
Fixed an issue that prevented downloading files from analyses launched with the Microarray Analysis Setup tool.
Release 7.8.1 - January 26th, 2022
Features
None.
Bugs Fixed
Performance and stability fixes.
Updated the BaseSpace Downloader to version 3.0. For more details, see What's New.
Added the 'DRAGEN Server' analysis location in Run Planning. Use this option to export the sample sheet to analyze sequencing data on a standalone DRAGEN server.
Manual mode runs from NovaSeq X and MiSeq i100 instruments without a sample sheet will now transition to 'complete' following upload. Previously these runs were marked as 'needs attention'.
Improved performance when loading the Microarray Analysis Setup tool.
Bugs Fixed
Fixed an issue that could cause a "Separator must begin with the + sign" error when uploading a FASTQ file.
Fixed an issue that could cause a run or project transfer to become stuck.
Fixed an issue with the Analysis file browser that could cause files to display under the incorrect folder.
Fixed an issue that could cause a run status to stay 'Pending Analysis' after analysis aborts.
Fixed an issue in Microarray Analysis Setup where file upload was silently failing.
Fixed an issue in the Analysis list page Application filter that showed duplicated application names.
Fixed the Application filter in the Analysis list page to include the ICA Workflow Session Tracking app.
Fixed an issue when launching an analysis from the CLI where the default analysis name is not generated correctly.
Known Issues
The copy and merge features are currently unavailable for samples generated by BCL Convert.
Added an "ICA Orchestrated Analyses" section to the Analysis Details page for autolaunched analyses. The section displays the status and details of each individual analysis launched.
Added a link to Usage Explorer in the header waffle menu.
Switching to the Usage Explorer now retains the current workgroup context. Only admins can see workgroup or domain-level usage.
Bugs Fixed
Fixed an issue in the Analysis Files tab that occurred when multiple datasets with the same name existed, causing only one to be displayed.
Fixed an issue that could prevent pricing information from displaying on the App details page.
Fixed an issue that could prevent an app from transitioning to 'Complete' when no output datasets were produced.
Fixed an issue on the Analysis Details page that could display a link to a Project the user does not have access to, resulting in a 403 Forbidden page when clicked.
Known Issues
The copy and merge features are currently unavailable for samples generated by BCL Convert.
Improved performance when post-processing analysis results from certain apps.
Added support for custom configuration files in the Microarray Analysis Setup tool.
Bugs Fixed
Fixed an issue that could cause an extra 30-day over-limit auto-deletion email to be sent when an account is eligible for deletion.
Fixed an issue on the Run Biosamples tab where the FASTQ Dataset link routed to the Biosample Other Datasets tab.
Fixed an issue that could cause a bad URL to route to an "unexpected issue" page instead of a 404 page.
Fixed an issue that prevented Runs from moving to Needs Attention status if the FASTQ Generation analysis timed out.
Fixed an issue that could cause a dialog box to briefly display before closing on its own when an error is returned.
Fixed an issue in Microarray Analysis Planning where the launch analysis button is available after removing the sample sheet.
Fixed an issue that prevented errors from displaying when updating metadata for a custom reference file.
Fixed an issue where uploaded runs incorrectly had status 'Needs Attention' with an error indicating a custom samplesheet is missing.
Fixed an issue where some genomes in Resources page cannot be downloaded.
Numerous table columns on Run and Biosample pages can now be resized.
Bugs Fixed
Fixed an issue that could cause an incorrect run selection when sorting a table after making selections.
Fixed an issue that prevented users from selecting and copying values within tables.
Fixed a display issue that prevented users from seeing all the content in certain modal windows.
6.3.0
November 10, 2020 - 6.3 - Notification Menu
Features
6.13.0
September 21, 2021 - 6.13 - NovaSeq Run Setup Support
Features
6.9.0
May 25, 2021 - 6.9 - Subscription Details
Features
5.33.0
April 2, 2019 - 5.33 - Performance Improvements
Features
5.42.0
January 23, 2020 - 5.42 - Biosample rename and gzip upload support
Features
5.24.0
July 17, 2018 - 5.24 - Display and Filtering Bug Fixes
Bugs Fixed
Fixed an issue that could cause selected rows to appear unchecked after horizontally scrolling a table.
Added a notification menu for non-spotlight notifications.
Added % Loading Concentration metric.
Added support for TSV format for custom index adapter kits created in Instrument Run Setup.
Added On Hold status for biosamples.
Added biosample status changes to audit logs.
Bugs Fixed
Fixed an issue where the TotalCount field of the appsession API endpoint returned an incorrect value.
Fixed an issue that prevented the preferred version to be set for some applications.
Fixed an issue that could cause pop-up modals to run off the page.
Fixed an issue on the Search page that could cause the filter panel to not load properly.
Fixed an issue that would display "Invalid date" instead of a timestamp in certain browsers.
Fixed small cosmetic issues on app launch pages.
Release 6.3.1 - November 16, 2020
Features
Performance improvements.
Bugs Fixed
Fixed an issue where not all workgroups are listed when logging in from an instrument.
Fixed an issue where tooltips did not display correctly on the Run Metrics page.
Fixed issues that could cause the Run Sample Sheet tab to not load properly.
Instrument Run Setup now supports generating NovaSeq sample sheets. (Staged rollout complete Oct 1 2021)
Released BCL Convert version 1.3.0. View the app and detailed release notes here.
Released BaseSpace command-line interface (CLI) version 1.4.1. Download here or view detailed release notes.
Performance improvements and fixes.
Bugs Fixed
Fixed an issue on the Biosample master list where the Biosample name was displayed in the Project column.
Fixed an issue in the Active runs list where the Transfer Ownership call to action remained enabled when that transfer was already pending.
Fixed an issue in Instrument Run Setup where the loading spinner disappears before the required APIs are loaded.
Fixed an issue that could cause a resource to be stuck in the Archived state.
Fixed an issue that would incorrectly display an error message when copying a shared FASTQ dataset.
Release 6.13.1 - September 24, 2021
Features
Performance and stability improvements.
Bugs Fixed
Fixed an issue on the Instrument Run Setup page that blocked the Next button when run names started with numbers.
Added the % Reads Identified chart to the Indexing QC page.
The Account Overview settings page now displays subscription expiration date, subscription status, and iCredit balance.
Changed instrument-specific option label in New Run menu to "Instrument Run Setup".
Improved Instrument Run Setup user experience when importing a sample sheet with a defined Index Adapter Kit.
Bugs Fixed
Fixed an issue with the default order of entries on the Demo Data page. Entries are now sorted chronologically with newer entries listed first.
Improved messaging for sample report generation failure.
Fixed an issue that caused the Upload Biosample Manifest modal to close when users click outside the modal.
Fixed an issue that disabled dataset links on the Run Biosamples page.
Fixed an issue that showed an empty Run Biosamples page for projects owned by another user.
Fixed an issue on the Run Metrics page where the table headers did not display after saving the metrics as a PDF.
Performance Improvements.
Bugs Fixed
Added error messaging that displays when a file download attempt is made on an unsupported system.
The UI file uploader now supports gVCF and gzipped VCF files.
The app input form now displays a notice if a newer version of the app exists.
The owner of a biosample can edit the biosample name. To rename the biosample, select the File menu, point to Edit and then select Biosample Info.
Bug Fixes
Fixed the status field requirement in the POST /v2/libraries/{id} endpoint. The status field is now optional instead of required.
Fixed an issue with the applications API returning an incorrect total count when getting a list of applications.
Fixed an issue with the Classic/New banner information icon in the Frankfurt/EU instance incorrectly linking to the US help files.
Fixed an issue with the My Illumina selection redirecting to the last-visited Illumina page instead of the account settings page.
Fixed a display issue with data point tooltips in Run Charts not displaying on screen.
Fixed a display issue with the FASTQ file upload library prep kit dropdown. The list of the display is widened to fit long prep kit names.
Fixed a filtering issue in New mode. The .bed filter in the app input file chooser incorrectly returned .txt files in addition to .bed files.
5.40.0
November 19, 2019 - 5.40 - Run Name Editing
Important: Account Data Deletion
We are turning on data deletion for inactive free accounts that have not logged in for 180 days or more.
The system will send email notifications to inactive accounts warning them, and users have 30 days to reactivate their accounts by logging in.
Features
Enabled editing run names from either the run details page or the run master list (File | Edit | Run Info).
Renamed thePending Execution status to Queued for Analysis, and clarified the status tooltip description on the analysis master page.
Bug Fixes
Fixed an issue that allowed share recipients to update the status of a run.
We now are calculating project storage size based on Datasets instead of Samples and Appresults, this should be more accurate but may result in changes for some users. Staged roll out, estimated completion is 1/1/2020.
Release 5.40.1 - November 26, 2019
Features
None.
Bug Fixes
Release 5.40.2 - December 4, 2019
Features
Bug Fixes
Bug Fixes
Release 5.40.3 - December 9, 2019
Features
None.
Bug Fixes
6.6.0
February 16, 2021 - 6.6 - Improved Sample Sheet Handling
Features
V2 Sample Sheet runs that are in Needs Attention status now display error messages.
Improved messaging for sample sheet import errors in Instrument Run Setup.
Released BaseSpace command-line interface (CLI) version 1.3.0. or view release notes .
Bugs Fixed
Fixed Manage Workgroups URL for Enterprise users.
Fixed an issue that would dismiss a shared invitation for a project while accepting the invitation for a different one.
Fixed an issue that could cause a FASTQ dataset to link to multiple libraries.
5.21.0
May 30, 2018 - 5.21 - Improved Yield Status Information on Biosample Summary Page
Features
Updated Latest Yield section of the biosample summary page to display more relevant yield values.
Bugs Fixed
Fixed an issue with the file downloader failing to find multi-node FASTQ analysis files.
Fixed an issue with the loading spinner on the analysis metrics page continuously displaying after sorting by column header.
6.2.0
October 13, 2020 - 6.2 - Instrument Run Setup Enhancements
Features
Added the selected analysis name and version to the Analysis Setup section of Instrument Run Setup
Added description of selected library prep and index adapter kits below each field in Instrument Run Setup.
Increased the character limit for project names to 255.
Bugs Fixed
Fixed an issue on the Run list that could cause a blank popup to appear when filtering a column.
Fixed an issue that could cause users to revert to the personal context while in a workgroup.
Fixed an issue that caused the delete menu option to be disabled for shared runs.
Added FASTQ Datasets and Other Datasets tabs to the projects page. Other Datasets includes uploaded files, and app files that are not part of a biosample.
Added Run and Flow Cell ID data to the biosample dataset tooltips.
Added banner notifications for expiring or expired subscriptions.
Updated the share link deactivation confirmation to include information about managing user access after the link is deactivated.
Adjusted the display of base pair numbers. When the number of base pairs exceeds 1000 Gbp, the scale is adjusted to display in Tbp.
Bug Fixes
Fixed an issue where FASTQ validation continued after a file upload was cancelled.
Fixed an issue that allowed setting a library's prep kit to a deleted kit
Release 5.36.1 - July 22, 2019
Features
Updated docker.illumina.com to support Enterprise apps (staged release complete 2019-08-06).
Performance improvements.
5.26.0
September 11, 2018 - 5.26 - Storage Limit Banner Notifications
Features
Added banner notifications for Basic accounts that have exceeded data storage limits.
Improved text formatting in the screens for uploading miscellaneous file types.
Improved design of the available app selection list for launching apps.
Bugs Fixed
Fixed an issue with FASTQ Generation failure when processing NovaSeq data with 384 samples per lane. FASTQ Generation can now process up to 1000 samples per lane for NovaSeq. Staged roll out complete.
Fixed an issue that caused Analysis summary pages to hang.
5.28.0
November 8, 2018 - 5.28 - Improvements to File Upload, Run Data Display, and Search
Features
Added more run, status, and QC data to the Run Summary page.
Improved file upload to support encrypted manifest (*.emf) files and AmpliSeq for Illumina manifests.
Improved the Analysis Master List display. Column data is automatically resized when the filter widget is activated so that table columns are not obscured.
Improved the search function to include flow cell ID. Searching by flow cell ID now returns associated runs even if the run name does not contain the flow cell ID.
Updated www.basespace.illumina.com to redirect to the BaseSpace Sequence Hub login page at https://basespace.illumina.com/auth/logon.
Bugs Fixed
Fixed sample pair selection to allow more than one pair to be created via drag and drop.
Improved Runs list page loading times. Pages with a large number of rows now load content continuously as you scroll.
Release 5.28.1 - November 15, 2018
Features
Internal release, no changes in functionality
Bugs Fixed
6.4.0
December 15, 2020 - 6.4 - Per-sample Analysis Settings
Features
Added support for per-sample settings in the Run Setup tool to configure analysis settings for individual samples.
In the Run Setup tool, the FASTQ Generation analysis type is now named BCL Convert.
Improved support for detecting errors in V2 Sample Sheets. Critical errors now transition the run to Needs Attention status.
Performance improvements to BCL Convert integration for NextSeq 1000 & NextSeq 2000 systems.
Bugs Fixed
Fixed an issue where index and library kits were changed to unspecified kits when editing a planned run in the Run Setup tool.
Fixed an issue with Run Setup tool where analysis settings were not refreshed after changing analysis type.
Fixed run setup to remove leading or trailing spaces in run name, sample ID, index, or free-text fields in the Run Setup and Analysis Setup pages.
7.19.0 - Transfer of NovaSeq X Projects
Feb 27, 2024
Features
Added the ability to transfer Projects containing autolaunched NovaSeq X analysis data and output from ICA pipeline-based apps (staged rollout complete February 29 2024).
Updated the Microarray Analysis Setup ‘Import SampleSheet’ function to allow for additional columns in sample sheet.
A new version of the BaseSpace Downloader for Windows has been made available, that fixes network connection issues experienced by some users. Users will be prompted to upgrade to the new vesion (2.2.8.0) when they next launch the Windows downloader.
Bugs Fixed
Fixed an issue that could prevent a Run's status from updating when an associated analysis times out.
Fixed an issue that could occur when launching apps from FASTQs generated by BCL Convert or NextSeq1000/2000 autolaunch.
Fixed an issue that caused the Requeue > Planned Run menu option to be enabled for shared Runs.
5.43.0
March 3, 2020 - 5.43 - NextSeq 1000/2000 Instrument Run Setup
Features
Prep tab is renamed to Run Planning and includes two menu options: Instrument Run Setup (supporting NextSeq 1000 and NextSeq 2000 systems) and the original Prep page for other systems.
Changed billing options for third-party apps. Billing is disabled for new apps and pricing for existing apps cannot be changed.
Increased the number of supported characters for adapter sequences to 128.
Bug Fixes
Fixed an issue that would cause an error when a custom name was used for a sample sheet.
Fixed an issue in the Move Runs to Trash dialog that allowed more than one option to be selected.
Fixed an issue where long app names were shortened in the header of app input forms.
Release 5.43.1 - March 4, 2020
Features
None.
Bug Fixes
Release 5.43.2 - March 18, 2020
Features
None.
Bug Fixes
Release 5.43.3 - March 23, 2020
Features
None.
Bug Fixes
7.29.0 - Improved Analysis Error Reporting
December 17, 2024
Features
Added improved error reporting for supported analyses, such as those auto-launched from NovaSeq X and MiSeq i100 instruments. A link in the logs section of the Analysis Summary tab opens a modal displaying a list of failed steps and relevant log file contents.
Bugs Fixed
Fixed an issue that could cause analyses to complete before all datasets are created.
Improved the messaging for certain errors that could occur when requeueing an analysis in Run Planning.
Fixed an issue that could cause an 'unknown settings found' error after selecting a BCL Convert version in Run Planning.
Known Issues
When running MacOS Sequoia, the BaseSpace Downloader throws an error on download. Leaving the Downloader open and retrying will allow it to start successfully.
5.44.0
March 31, 2020 - 5.44 - Improvements in Instrument Run Setup
Features
6.8.0
April 20, 2021 - 6.8 - Run Charts Improvements
Features
6.1.0
September 15, 2020 - 6.1 - Archival Storage
Archival Storage Feature
6.0.0
August 11, 2020 - 6.0 - BaseSpace Sequence Hub 6.0
November 16, 2021 - 6.15 - Microarray Anaysis Setup
Features
5.23.0
June 26, 2018 - 5.23 - Publishing Apps to your Enterprise and Faster SAV Downloads
Features
7.28.0 - MiSeq i100 Support
November 19, 2024
Features
7.26.0 - Prep Tab Obsolescence Notification
September 17, 2024
Features
Renamed the run summary
Avg %Q30
metric label to
% ≥Q30
.
Fixed an issue that prevented the download of analysis results.
Performance and stability fixes.
Performance and stability fixes.
Fixed an issue that caused a failure to delete error message to appear after a planned run was successfully deleted.
Fixed an issue in the Planned Run list that would display Index2 length values for single index runs.
Fixed an issue that caused dropdown menus in Instrument Run Setup to display truncated names.
Improved performance of the /v2/preprequests API endpoint.
Fixed an issue with app input forms that could cause choosers to remain available when nested in a radio component.
Fixed an issue where uploading runs from both sides of a HiSeq flow cell could cause duplication of the project name.
Security Fixes
Bugs Fixed
None.
Fixed the dashboard widget and usage reports to correctly display the number of iCredits used for app purchases.
Fixed the runs list display of run sizes larger than 1 TB. The run size is now rounded to two decimal places.
Fixed an issue that caused chart displays to load slowly. As a result, the InterOp folder now includes a cache subfolder that contains additional files.
Improved the usability of the BaseSpace app launch pages. Some input fields have been widened to increase legibility.
Fixed the display of the settings page loading icon, which was appearing in duplicate.
Fixed sample pair selection to allow more than one sample pair to be created using drag and drop.
Fixed minor page display issues.
None
Fixed an issue that could cause the dashboard to display a warning message for exceeding "0 Bytes storage limit".
Fixed an issue on app input forms where clicking a tooltip by a checkbox item also selected or deselected the checkbox.
Fixed an issue that could cause an error when removing a shared project.
Fixed a display issue that caused the App Purchase dialog to extend off screen.
Fixed an issue that could prevent accepting share or transfer invites.
Fixed an issue that limited the number of analysis files displayed in the UI to the first 100.
Fixed a performance issue with processing sequencing run metrics.
Fixed an issue in the sequencingstats endpoint that caused PercentNoCalls values to be set to 0.
Fixed an issue that caused ICA pipelines to fail when launched with a biosample with no default project.
Fixed an issue in Microarray Analysis Setup where the page is not reset after changing the workgroup context.
Fixed an issue in Microarray Analysis Setup that causes the Load Samples modal to remain open after importing duplicate idats.
Fixed the display of yield records when all data sets are deleted. The yield record is now removed entirely instead of displaying 0 bp.
Performance and stability fixes.
Fixed an issue that could occur while deleting a dataset.
Prevented an intermittent error message that could appear when accessing the website.
Fixed an issue that caused the requeue menu option to be enabled for monitoring-only runs.
Fixed an issue that prevented node statuses from updating automatically on the Analysis Details page.
Fixed inconsistent timestamp formats on the Analysis Details page.
Added a default Select option to drop-down menus in the Analysis Setup page for Instrument Run Setup. This option can be used to clear an unwanted menu selection.
Bug Fixes
Improved Prep tab error messages for duplicate sample names in imported library templates.
Fixed an issue that prevented display of Indexing QC if a run did not have Indexing QC data for the first lane.
Fixed an issue where reports generated from multi-node app sessions did not display until the page was refreshed.
Fixed an issue that caused slow uploads of custom files in Instrument Run Setup.
Security improvements.
Release 5.44.1 - April 8, 2020
Features
Updated the support team contact information in the "Activate Subscription" dialog box.
Bug Fixes
Performance and stability fixes.
Release 5.44.2 - April 11, 2020
Features
None.
Bug Fixes
Performance and stability fixes.
Release 5.44.3 - April 20, 2020
Features
None.
Bug Fixes
Performance and stability fixes.
Release 5.44.4 - April 23, 2020
Features
None.
Bug Fixes
Performance and stability fixes.
Performance improvements to the Run Charts page.
Added a link to analysis and storage pricing information in the Instrument Run Setup tool.
Share and transfer invites that are sent to an email address before the account is created now appear on their first login.
Added the option to share associated projects when sharing a run with other accounts.
Bugs Fixed
Fixed an issue in the FormBuilder that prevented the display of section breaks.
Fixed an issue in the FormBuilder where FieldSet components ignored the "isOpen" field.
Fixed an issue that prevented the deletion of planned runs.
Fixed an issue where file preview modals were too small when previewing image files.
Fixed an issue that prevented a biosample from showing up in a chooser after marking its FASTQ dataset as QC Passed when the FASTQ dataset previously failed.
Fixed an issue on the Appsession Reports page that displayed a per-sample report by default, instead of the summary report.
Fixed an issue that allowed multiple clicks of the Accept button in share invitations.
Fixed an issue where the lock icon was missing on the summary page for biosamples with datasets from multiple sources.
Fixed Run and Biosample master list issues that prevented column selections from being saved.
Fixed an issue where the notification bell obscured the app name in lower display resolutions.
Fixed an issue where the Download option was enabled for runs in an Uploading state.
Release 6.8.1 - April 29, 2021
Features
Performance improvements.
Bugs Fixed
Fixed an issue where ICA-based apps would fail when launching through a biosample workflow.
Release 6.8.2 - June 3, 2021
Features
Performance and stability improvements.
Archival storage is being rolled out to users over the next few weeks. This feature allows accounts configured for New application mode to transfer runs and datasets to long-term storage, with significantly lower costs than standard storage. Data transfer takes several days to complete and incurs additional fees. Restoring data that have been archived for a short period of time can result in higher overall storage cost, so archiving is not recommended for data that you intend to use in the next several months.
Other Features
Added iCredit balance and subscription status to the account settings page.
Added promotional iCredit balance to the banner notification in Free Trial accounts.
Bugs Fixed
Create new project option not enabled on the Prep tab page for creating a biological sample.
Error when downloading files or sharing data in Enterprise domain accounts.
Incorrect items listed in the Status menu.
Runs page tabs content failed to load if the run name contained special characters.
The list of libraries did not appear on Pools pages.
Menu dropdown failed to close after a selection was made.
Runs page column settings reset to default after a page refresh.
Run details page did not display share and trash menu options.
Tooltip for multiple pool information failed to appear on biosample libraries page.
Incorrect link to BSVI in the waffle menu.
Overlapping text in the Run details Sample Sheet tab.
Banner notification did not persist across pages.
Release 6.1.1 - September 16, 2020
Features
None.
Bugs Fixed
Fixed an issue that could cause the Run name to become hidden in the Run master list.
Performance and stability fixes.
Release 6.1.2 - September 18, 2020
Features
None.
Bugs Fixed
Fixed an issue that could cause some run metrics to be displayed incorrectly.
Performance and stability fixes.
Improved integration of cloud-based analysis for NextSeq 2000 systems.
Bug Fixes
Fixed an issue that could cause an empty red banner to display for Basic user accounts that are near or over the storage limit.
Release 5.46.1 - July 16, 2020
Features
Increased the number of files displayed in the Analyses page file browser to 2,048.
Bug Fixes
Performance and stability fixes.
Release 5.46.2 - July 17, 2020
Features
None.
Bug Fixes
Fixed an issue that could block summary reports from displaying.
Performance and stability fixes.
Added Files & Kits menu to the Settings page, where the following run setup resources can be viewed or added:
Library prep kits
Index adapter kits
Reference genomes
When running a NextSeq 2000 in Local Analysis mode, uploaded analysis results are stored in a project. If a project does not exist, a new project is created.
Improvements to Run Setup:
Added support for large file upload.
Added confirmation prompt when switching Analysis Type or Analysis Location.
Added display of additional details when a reference genome is selected.
Bug Fixes
Fixed an issue that caused the My Data and Run Planning navbar links to briefly duplicate on page load.
Fixed an issue with multi-node appsessions where the report did not display until the page refreshed.
Fixed an issue with the dataset matcher that prevented tooltips from displaying.
Fixed an issue that created duplicate planned runs if Submit was selected more than once in the Run Setup tool.
Fixed an issue where editing a planned run with unspecified kits did not have the correct columns in sample data table.
Fixed a bug where using an unacceptable character (".") was not prevented during run setup.
Fixed an issue where a 'required field' error message could appear erroneously during run setup.
Fixed a rare issue that could prevent app launches.
Security fixes.
Release 5.45.1 - May 28, 2020
Features
None.
Bug Fixes
Performance and stability fixes.
Updated the look and feel of the Settings pages.
Improved behavior when creating a new Project in a Project Chooser modal. Creating a new Project automatically selects it and closes the modal.
Improved Project support when using the V2 Sample Sheet format. The optional ProjectName column is now used for Biosample Default Project and Output Project, when specified.
Bugs Fixed
Fixed an issue that could prevent appsession logs from being displayed.
Fixed an issue on app input forms that caused the Add a New Row button to be invisible in Safari.
Fixed an issue on the Run Metrics tab where the Tbp unit was not being used for yield values above 1000 Gbp.
Fixed an issue that could cause an appsession encountering an error to get stuck in the initializing status instead of aborting.
Fixed an issue on the Run Metrics page where the cluster density standard deviation value was not adjusted to the same scale as the density value.
Release 6.5.1 - January 27, 2021
Features
Performance improvements.
Bugs Fixed
None.
Separated the Biosample Datasets tab into two new tabs: FASTQs and Other Datasets.
Updated the look and feel of the Biosample Analyses tab.
Released BaseSpace command-line interface (CLI) version 1.4.0. Download here or view detailed release notes.
Bugs Fixed
Fixed an issue that could redirect users to a 403 page when copying FASTQ Datasets into a shared project.
Fixed an issue that could cause the Biosample Details page to refresh when loading.
Release 6.10.1 - June 30, 2021
Features
Performance and stability improvements.
Improved look and feel on the dashboard, runs spotlight section, navbar, and toolbar menus.
Updated the toolbar icons.
Added the option to switch to the correct Workgroup when following a Project or Analysis link.
Added the application category "Infectious Disease + Microbiology".
Added an analysis description in Microarray Analysis Setup that displays after selecting an analysis.
Updated the dropdown lists in Microarray Analysis Setup to sort alphabetically.
Bugs Fixed
Fixed an issue that could prevent Run size from updating during upload.
Fixed an incorrect validation for the Override Cycles field in Run Planning that prevents user from setting up a run with Index1 as UMI and Index2 for demultiplexing.
Fixed an issue in Run Planning that occurred when importing a NextSeq1000/2000 planned run from a sample sheet that does not contain an OverrideCycles value.
Fixed an issue in Microarray Analysis Setup where a "Failed to import idats" message remained after re-importing valid files.
Fixed an issue in Microarray Analysis Setup where uploading an invalid Product Descriptor file would cause the Add Custom Configuration modal to hang.
Microarray Analysis Setup is now available in the New Run dropdown menu.
BaseSpace command-line interface (CLI) version 1.5.0. Download here or view detailed release notes.
Custom fixed layout single index kits are now supported in the run setup tool.
Bugs Fixed
Fixed an issue that caused the /v2/feeds endpoint to return an error.
Fixed an issue that could cause toolbar menu actions to stay disabled when on the Run master list.
Fixed missing "copy" icon on the Share By Link modal.
Added the ability for Enterprise users to publish apps to their domain. Apps published in a domain through the Developer Portal will only show up for users in the domain.
The performance of SAV download of run InterOp files has been improved by only downloading aggregated files when available. When aggregated files are not available, per cycle files will downloaded.
Bugs Fixed
Fixed an issue where a user could be prompted with the window to accept an app's EULA after accepting it already.
Fixed an issue with workflow analyses getting stuck in "Pending Execution".
Release 5.23.1 - June 28, 2018
Bugs Fixed
Fixed an issue displaying reports for multi-node apps.
Added support for the MiSeq i100 and MiSeq i100 Plus instrument types.
Redesigned the Analysis Summary tab. For more details, see What's New.
Added the release version and a release notes link to the site footer.
Added the ability to preview .command.out and .command.err files in the analysis file browser.
Updated the BaseSpace CLI to version 1.6.2. Download the latest version and see the release notes here.
Bugs Fixed
Fixed an issue that could cause runs to get stuck in 'Pending Analysis'.
Fixed a rare issue that could cause analyses to become stuck in 'Initializing'.
Fixed an issue that could cause certain analyses to stall and time out after encountering an error, rather than aborting.
Fixed an issue that could associate a Biosample's Default Project to an Analysis even if no results were output to the project.
Fixed an issue that could prevent the association of a Biosample to a Project when FASTQ data was generated.
Fixed an issue that could cause certain analyses to hang when cancelled during post-processing.
Fixed an issue that allowed analyses in non-terminal statuses (eg, running) to be moved to the trash.
Fixed an issue when searching for a file name that caused a "No matching records found" message to display after clicking the search link.
Fixed an issue that prevented some application icons from displaying properly.
Known Issues
When running MacOS Sequoia, the BaseSpace Downloader throws an error on download. Leaving the Downloader open and retrying will allow it to start successfully.
Pasting data into the Sample table of Run Planning (e.g., from Excel) does not populate the fields.
Release 7.28.1 - December 3, 2024
Features
None.
Bugs Fixed
Restored the ability to paste data into the Run Planning Sample table.
Fixed an issue affecting the display of Indexing QC metrics for NextSeq1000 and MiSeqDx instruments.
Fixed an issue that could prevent project links from appearing on the Analysis Summary tab.
Prep functionality is being deprecated. Starting in January 2025, the Prep tab will no longer be available. Most users have already upgraded to use Run Planning. It is recommended any legacy NextSeq and MiniSeq users update to the latest software releases for their platform.
Archive is now available for all runs and datasets, including data from NovaSeqX and NovaSeqXPlus instruments.
ICA analysis logs have been moved to a dataset called "ICA Logs", to make them easier to find in the Analysis Files UI.
Added the ability to requeue a Run from the Run list.
Bugs Fixed
Fixed an issue that prevented the index cycles from displaying on the Run Summary tab before the upload completed.
Fixed an issue that could cause a run with a bad sample sheet to get stuck in 'Pending Analysis' rather than moving to 'Needs Attention'.
Fixed an issue that allowed a run to be transferred before the upload completes.
Fixed an issue that could prevent the Run Indexing QC tab from displaying properly.
Fixed an issue that could send duplicate "run created" emails when starting a sequencing run.
Added initial support for integration with Illumina Connected Analytics (ICA), via a new app, BCL Convert for ICA Beta. This version exposes the generated FASTQ files and Samples within ICA.
Bugs Fixed
Fixed an issue that could cause the "Change FASTQ QC Status" dialog to load slowly.
Known Issues
FASTQ Generation and other apps very infrequently abort while uploading results.
For customers using Instrument Run Set up to create a v2 sample sheet for a NovaSeq SP 500 cycle run, the sample sheet produced has the I5 index sequence in the incorrect orientation. This assigns all sample reads to undetermined. To correct the issue, we recommend removing the "IndexOrientation Forward" flag from the [Header] section of the sample sheet.
Fixed display issues that misaligned or cut off biosample metadata.
Fixed an issue that prevented custom library prep kits from being deleted.
Fixed an issue on Demo Data pages that would show a blank page when no search results are found.
Fixed an issue that hid timed out appsessions from the analysis master list.
Fixed an issue that prevented appsessions from timing out.
Fixed an issue that caused miscellaneous (ie, non-manifest) .txt files to be treated as manifest file type instead of misc file type when uploading to a project, resulting in rejection due to failed validation.
Version 6.0.0 implements a new look, aligned to the latest instrument design, and improvements to page loading speeds.
Dashboard spotlight displays items that require attention.
Run insights to track run metrics over time. View charts on the dashboard and export data to a CSV file. (Staged roll out completed August 12)
Run filters built in to column headers in the runs list.
Switching between Classic and New application versions is enabled in the Account Settings options.
Changes to support Classic mode:
My Data tab is removed. Items previously listed in the My Data menu are now primary tabs.
Run planning is moved to the Runs page.
Screenshot of the BaseSpace Sequence Hub 6.0 dashboard, showcasing the new user interface, spotlight section, and run insigts tool.
Bug Fixes
Fixed an issue that could cause a subscription renewal account banner to appear after a Professional subscription account is renewed.
Release 6.0.1 - August 12, 2020
Features
Added a link on the Apps page to the Developer Portal.
Bug Fixes
Fixed an issue that prevented planned runs from appearing in the Planned Runs tab.
Fixed an issue where the App bookmark icons were not always appearing.
Fixed an issue that could cause the Run Insights chart to display no data.
Release 6.0.2 - August 20, 2020
Features
Error messages from backend validation will be displayed for each field in the run setup page.
Dashboard includes a banner with free trial expiration date.
August 13, 2018 - 5.25 - ISO Date Display and Improved Project Master Page Appearance
Features
Dates and times are now displayed in ISO-compatible formats on the Dashboard, Runs list, Run Summary, and Run Files pages.
Removed folder icons from the projects master list to improve appearance. The Owner column lists the owner of projects shared with you. To view a list of collaborators in projects you own, select Share | Send Invitation from the project.
Biosample pages have been corrected to remove the term Registry, which is no longer used.
Bugs Fixed
Fixed a slow page loading issue in projects with large numbers of analyses.
Fixed Timed Out runs to allow requeues.
6.7.0
March 16, 2021 - 6.7 - Display V2 Sample Sheet Format
Features
The Run Sample Sheet tab now displays V2 sample sheet information.
Updated the look and feel of Run Chart and Biosample pages.
Added support for top-ups and requeues when automatically registering FASTQ data to ICA.
Bugs Fixed
Fixed an issue that could cause runs to have a size of "0". As a result of this fix, some users may see an increase in their overall storage usage.
Fixed an issue that could cause share links to not work correctly.
Fixed an issue that caused incorrect requeue options to be enabled for some NextSeq instruments.
Release 6.7.1 - March 22, 2021
Features
Performance improvements.
Bugs Fixed
7.2.0 - FastQ Generation and other Bug Fixes
June 22, 2022
Features
Performance and Security Improvements.
Reduced the time to abort analyses to 6 hours in cases where the post-processing step gets stuck. This change only affects a subset of BSSH apps.
Improved messaging when a user tries to trash an appsession within a shared project that the current user does not own. The message now will indicate that the individual shared resource cannot be deleted and advise the user to delete the entire shared project. If the user deletes the project, and are not the owner, the project will be unshared but remain in the owner's account.
Bugs Fixed
Fixed a rare issue where apps occasionally aborted with the message "Input JSON file not found." Any apps that previously aborted with this message will now proceed to completion without any additional user intervention.
Fixed an issue that could prevent trashing analyses with a large number of datasets.
Fixed issue that could cause moving appsessions with long names to the trash to fail.
5.22.0
June 12, 2018 - 5.22 - Associate Biosamples With Uploaded Files and Show/Hide Columns on Runs Page
Features
Added an option to associate a file (or dataset of files uploaded together) with a new or existing biosample during file upload.
Added an option to show or hide columns on the runs page, and added sort function to additional columns.
Bugs Fixed
Fixed an issue with library prep kits not appearing in the Multiple Kits drop-down list when selecting a biosample in the app input form.
Release 5.22.1 - June 14, 2018
Bugs Fixed
Fixed an issue with BaseSpace menu navigation to different software products. The links have been restored and you are now successfully transferred to the selected product.
5.27.0
October 2, 2018 - 5.27 - Analysis List Filters and UTC Timestamps
Features
Added Delivery Status and Project filters to Analyses List Page.
Added messaging to the Transfer Ownership dialog to clarify that the Optional Message text field supports 140 characters.
Added UTC-formatted timestamps to the Dashboard, Runs list, Run Summary tab, and Run Files tab.
Bugs Fixed
Fixed an issue that caused free apps to be disabled for Basic account users.
Fixed an issue with the app input form returning an error. If a FASTQ data set associated with an input biosample had been deleted, the app failed to launch. This issue occurred in New mode only.
Release 5.27.1 - October 29, 2018 - staged roll out complete
Features
Changed the compute instance type used by default for apps because AWS is deprecating the existing type. Thew new type is a more powerful instance with more cores and typically faster run times and lower costs. Please note that we have not been able to test all the apps, but have not seen issues with the illumina apps that we were able to test with the new instance type. Affected illumina apps (not labs apps) have an updated "What's New" section.
Bugs Fixed
5.30.0
January 24, 2019 - 5.30 - NovaSeq SP Charts
Features
Updated the Charts tab to support NovaSeq SP runs.
Improved display of Biosample details and File Upload pages.
Added the project name to HTML title for the Project page.
Bugs Fixed
Biosamples created in multi-node FASTQ Generation were missing from the Run Samples tab in Classic mode. The biosamples are now listed in both New and Classic modes.
Improved detail for some file upload error messages.
Some successful file uploads briefly displayed an error message in Firefox browsers.
Cluster count values were displayed incorrectly in the Run Master List popup. The correct values are now displayed.
Security improvements in the developer portal.
Release 5.30.1 - January 30, 2019
Bugs Fixed
Fixed a slow loading issue on Analysis results pages.
Fixed an issue where an incorrect ID was returned for analyses launched via v2 API and CLI.
6.12.0
August 18, 2021 - 6.12 - Unspecified Kit Index Validation
Features
Added duplicate index sequence validation in sample tables when the kit is unspecified.
Bugs Fixed
Fixed an error that could occur when downloading a reference genome from the Settings page.
Fixed an issue that would not display indexing QC metrics when a run completes.
Fixed an issue that could cause an app to abort while initializing.
6.14.0
October 26, 2021 - 6.14 - Updated Javascript Interpretation Library
Features
7.20.0 - Analysis List Improvements
Mar 19, 2024
Features
5.38.0
September 4, 2019 - 5.38 - BS CLI v1.0.0
Features
5.21.1
May 30, 2018 - 5.21 - Improved Yield Status Information on Biosample Summary Page
Features
5.32.0
March 12, 2019 - 5.32 - UI Improvements and Bug Fixes
Features
Fixed an issue that caused analysis workflow metrics and QC data to be removed if the associated analysis was deleted.
Fixed the default file sorting on run and analysis file pages.
Fixed an issue where users were not redirected to the dashboard after deleting a shared run or a run they own from their account.
Fixed an issue where cluster density values were cut off on the Run Metrics tab.
Fixed a performance issue that could occur when using the Copy > FASTQ Dataset feature.
Fixed an issue that prevented users from returning to a workgroup context when logging back into BaseSpace Sequence Hub.
Fixed an issue on the Runs master list where long run names would block the run details tooltip.
None.
Fixed an issue where the share/transfer acceptance modal displayed workgroups from other regions.
Fixed slow loading times on Runs list pages.
Disabled the Reports tab for apps that do not include report output. Application results are available on the Files tab.
Changed the Prep tab index edit icon to a pencil.
Fixed an issue running DESeq2 with blank entries in sample matcher.
Coverage files are no longer created from indexed bam files, resulting significantly shorter run times for apps that produce them.
Fixed an issue where the View Files link for logs for some analyses did not appear on the Analysis summary tab.
Fixed an issue that could show duplicate files in the Run tab.
Updated the Jint javascript interpretation library from v0.9 to v3.0. For more information, view the App JavaScript FAQ.
Biosample yields now stop calculating when 50 or more distinct libraries are associated.
Instrument Run Setup now supports specifying duplicate indexes in separate lanes for multi-lane instruments.
Updated the user interface with the following changes:
Added a link to the Admin Console in the User menu for admin users.
Moved the link to My Illumina from the User menu to the waffle menu.
Bugs Fixed
Improved reporting of JavaScript errors to app developers in the Developer Portal.
Fixed an issue where the Change Lane QC modal did not open.
Fixed a rare issue that could prevent sharing or transferring of Projects.
Fixed an issue that could prevent an appsession from being aborted after the 7 day limit.
Native App engine update - Staged roll out
Improved error handing and performance
Fixed an issue where FASTQ Generation and other apps could fail while uploading results.
Release 6.14.1 - November 1, 2021
Features
None.
Bugs Fixed
Fixed an issue that could cause apps to fail to launch.
Added the ability to filter the Analysis list page by Application.
Added resizing for the following columns in the Analysis list:
Name
Application
Project
Added the ability to define a custom product when creating a custom configuration in Microarray Analysis Setup.
Bugs Fixed
Stability fixes.
Fixed an issue so the Dashboard 'Recent Activity' section only shows Runs and Analyses owned by the current user or workgroup.
Fixed an issue that could cause an incorrect error message to display on subsequent attempts to move an object to the trash.
Fixed an issue that caused a mismatch between the Analysis list 'Last Modified' timestamp and the Analysis details 'Date Completed' timestamp.
Fixed an issue that could cause analysis logs to display a FASTQ-related message even when no FASTQs were generated.
Updated the appearance of the Run Sample Sheet page.
Bugs Fixed
Fixed missing Project links on Analysis pages.
Fixed an issue that could cause newly created project files to be unavailable for download.
Recomputed yield on old samples to enable selecting them as application input.
BS CLI v1.0.0 released! Our command line tool has graduated to a supported illumina product. or read the documentation.
Filter FASTQ Datasets by Run on the FASTQ Datasets tab.
Clarified that iCredits figures on the dashboard refer to usage, not balance available
Clarified that billing date on the dashboard refers to the current monthly billing period end date
Bug Fixes
Fixed an issue where child app sessions were not always terminated when the parent app session was.
Fixed an issue that could prevent accepting a public project share.
Release 5.38.1 - September 18, 2019
Features
Performance and stability improvements.
Bugs Fixed
None.
Release 5.38.2 - September 25, 2019
Features
Performance and stability improvements.
Bugs Fixed
None.
Release 5.38.3 - October 2, 2019
Features
Performance and stability improvements.
Bugs Fixed
None.
Updated Latest Yield section of the biosample summary page to display more relevant yield values.
Bugs Fixed
Fixed an issue with the file downloader failing to find multi-node FASTQ analysis files.
Fixed an issue with the loading spinner on the analysis metrics page continuously displaying after sorting by column header.
Fixed an issue that caused miscellaneous (ie, non-manifest) .txt files to be treated as manifest file type instead of misc file type when uploading to a project, resulting in rejection due to failed validation.
5.39.0
October 17, 2019 - 5.39 - Improved performance of FASTQ file importing
Features
Improved performance of FASTQ file importing via web upload.
Bug Fixes
Fixed an issue that allowed projects with outstanding transfer invitations to be moved to the trash.
Fixed an issue where Run Name and Flow Cell ID did not appear in FASTQ Dataset tab tooltip.
Release 5.39.1 - October 28, 2019
Features
None.
Bug Fixes
5.37.0
August 6, 2019 - 5.37 - Improvements to FASTQ Datasets Tab
Features
Added Analysis name filter for FASTQ Datasets.
Added detailed error messages to the Move Analysis to Trash confirmation message.
Added run name column to the FASTQ Datasets tab.
Improved column alignment and spacing in Biosample list and Datasets tab.
Performance improvements.
Bug Fixes
Fixed an issue where the Manage Workgroups link did not appear for workgroup administrators.
Fixed an issue in the Runs master list where ordering the runs by owner failed to load.
Release 5.37.1 - August 9, 2019
Features
None.
Bugs Fixed
5.31.0
February 6, 2019 - 5.31 - Improvements to App Launch
Features
Improved launch of apps with up to 384 samples to avoid a time-out.
Workgroup administrators can now manage workgroups.
Bugs Fixed
When uploading a VCF with a file name that exceeds the character limit, the error message now indicates that the filename is too long.
Uploading files to the website over a slow internet connection no longer causes a time-out.
Release 5.31.1 - February 8, 2019
Features
Performance improvements.
Bugs Fixed
Release 5.31.2 - February 11, 2019
Features
Expected yield is now only calculated for biosamples with 32 datasets or less. For biosamples with more than 32 datasets, expected yield will equal the actual yield.
Bugs Fixed
Release 5.31.4 - February 26, 2019
Features
Performance improvements.
Bugs Fixed
Release 5.31.5 - March 6, 2019
Features
None.
Bugs Fixed
5.34.0
May 16, 2019 - 5.34 - Performance Improvements and Bug Fixes
Features
Performance Improvements.
Added the Illumina FASTQ File Upload Requirements help page link to the error message that appears when a user uploads a FASTQ file with an invalid naming convention.
Updated the Prep tab Biological Samples import page to include information about using library import when adding prepared libraries or samples with assigned indexes.
Bugs Fixed
Fixed an issue that could prevent app launch when using biosamples from an Illumina Public Data shared project.
Added error messaging that displays when a file download attempt is made on an unsupported system.
5.29.0
December 11, 2018 - 5.29 - FASTQ Filename Validation and App Bookmarking
Features
Added bookmarks to the app landing page. Bookmarked apps are listed in the sidebar adjacent to the apps list.
Added filename validation to uploaded FASTQ files. To prevent potential downstream app failure, the web uploader does not allow filenames that contain special characters.
A confirmation email is now sent when an inactive user reactivates their account by logging in.
Improved UI
Tabbed pages no longer display a subheader if the subheader is a duplicate of the tab name.
Initial Lane & QC Status label on the runs page is listed as Initial. Initial status was originally displayed as --.
The creation and updated dates for all resources in BaseSpace Sequence Hub are now formatted according to ISO-8601.
Bugs Fixed
Fixed an issue that caused problem when attempting to switch workgroups when the window size is small.
Fixed an issue that prevented some users from downloading project files when in New mode.
2019
6.16.0
December 14, 2021 - 6.16 - Trash Performance Improvement
Features
Fixed an issue where the dashboard link to the developer portal did not display for Enterprise users.
Fixed an issue where bookmarked apps might not appear in the bookmark widget.
Fixed an issue that caused long workgroup lists to load slowly.
Fixed an issue that could cause the workgroup list to hang indefinitely.
Fixed an issue that could cause the list of available workgroups to load slowly.
None.
Fixed an issue that could cause discarded fastq datasets to be submitted when launching apps with biosample inputs. Staged roll out completed Feb 12.
Fixed an issue that caused some apps get stuck in the "Payment Pending" state.
Fixed an issue where users were taken to an Unexpected Issue page when launching certain apps.
Fixed an issue in New mode that could cause apps to launch with incomplete FASTQ datasets.
Fixed an issue that could cause automatically launched workflows to immediately abort.
Fixed a formatting issue for long run names in the run master list run tooltip.
Fixed a formatting issue on analysis status tooltips.
Fixed some display issues in Safari.
Improved performance when moving large analyses to the trash.
Users can now review and accept the EULA when launching an analysis through Microarray Run Setup.
Bugs Fixed
Fixed an issue that could cause an app input form error when specifying uneven pairs in a Biosample matcher.
The file uploader now supports up to 250 GB in a single session. However, for large files, the BaseSpace command-line interface (CLI) offers significantly faster upload times.
Performance Improvements.
Bugs Fixed
Fixed an issue with empty biosamples not appearing in search results. Biosamples that have no data (no FASTQ data sets or all data sets are QC-failed) now appear in global search results.
Fixed an issue where links to deleted runs were not automatically removed from the Runs tab list.
Fixed an issue where the Yield calculation on the Run Summary tab was displaying the wrong unit of measure.
Fixed an issue where the analysis Inputs tab did not automatically refresh after an analysis was completed.
Fixed the default filters on the biosample chooser. When an app is launched from a project page, the available biosamples list is automatically filtered to show only biosamples from that project.
5.41.0
December 17, 2019 - 5.41 - 'User' Column in Run List
Features
Added a User column to the runs master list to indicate which user uploaded the run.
Enabled filtering in the projects Other Datasets tab.
Bug Fixes
Fixed an issue that could cause the biosample selection for app input to display an incomplete list of available biosamples.
Fixed an issue that could prevent the trash from being emptied properly.
Fixed an issue where the BaseSpace Downloader could not download files on OSX Catalina.
Release 5.41.1 - January 9, 2019
Features
None.
Bug Fixes
Performance and stability fixes.
7.24.0 - Requeue Improvements
July 23, 2024
Features
Improved the requeue experience for better consistency across runs and sample sheet formats. For more details, see .
Updated the BaseSpace CLI to version 1.6.1. Download the latest version and see the release notes .
Updated the UI to use more of the available screen width on larger displays.
Simplified the menu option for unzipping. To unzip a Run, select File > Unzip.
Bugs Fixed
Fixed an issue that could cause an analysis to abort when using a shared run as input.
Fixed an issue that could cause a project transfer to get stuck and prevent other actions.
Fixed an issue that prevented the developer tools from displaying in the developer portal form builder.
Fixed an issue where certain validations were not performed until after launching a requeue (eg, the run is transferring or in a non-terminal status). These validations are now performed after selecting the requeue option in the menu.
Fixed a typo in the Create Custom Library Prep Kit dialog.
