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Features
Increased the limit on the number of library prep kits displayed in the Prep Tab Library Prep Kit chooser
Bugs Fixed
Fixed a display issue with the project filter dropdown on the file chooser screen
Fixed links to run files lists
FASTQ Generation
Added support for NovaSeq S4 flow cell
Features
Updated the look of the apps page
Added ability to toggle between classic mode and new mode (see full notes on the new BaseSpace Sequence Hub below)
Bugs Fixed
Fixed issue with some access tokens unexpectedly changing workgroup contexts
Fixed issue with multi-select of libraries on the Create Pool page of Prep Tab
Our v5.6 release provides a new and other changes to support of previously time-consuming tasks. To try the new features, select New on the Dashboard page toggle button, or contact your workgroup owner to turn on the new features for you. for more information on the new features and updates.
The new features will be rolling out over the next few days.
UI Changes
Relocated Projects, , Runs, and Analyses under My Data in the navigation bar
Added an action toolbar throughout the app, where all functions like requeues, status changes, downloading, and sharing are accessed from
BaseSpace Sequence Hub 5.0 is a major update to support future enhancements in high-throughput sequencing operations and automation.
Prep Tab users will see new biosamples, libraries, and pools added to their Prep Tab lists as we begin preparing all users for the new automation features.
Added a Lane & QC Status to Runs and added the new status to the Filters widget
Added a Delivery Status to Analyses in order to manually track delivery of files to customers
Renamed Run & Lane Metrics to Metrics in the Run section
Renamed "Fix Sample Sheet and Requeue" to Requeue > Sample Sheet in the action toolbar
Renamed "Regenerate FASTQ" to Requeue > FASTQ Generation in the action toolbar
Added the ability to view details about an Analyses via a tooltip in the status column
Updated the Filter widget on the Analyses list
Updated the layout of applications on the BaseSpace Apps storefront screen
Added the filter widget to more lists so you can quickly narrow down to results that are relevant to you
Added inline tooltips throughout the application to provide additional helpful information
Added guided tutorials that demonstrate how to perform common actions via the Help menu
Added the ability to switch between the Classic and New versions of BaseSpace Sequence Hub via a toggle switch to the dashboard (only workgroup admins and owners of accounts can see this toggle). During the transition period you can switch to and from New and Classic as many times as you want. Please use the Email button on the bar containing the toggle switch to provide feedback if you experience any issues.
New Screens
Added separate screens that list all your Biosamples and Analyses
Added a Summary screen for each Biosample, along with dedicated screens for all associated Libraries, Runs, Requeues, Analyses, and Datasets for each Biosample
Replaced Samples with in the Projects and Runs sections
Launched to document all the new application features and make discovery of help topics easier
New Actions
Added the ability to Upload Biosample Workflows for creating biosamples with yield threshold requirements and setting up Automatic App Launches
Added the ability to pre-define metrics for Analysis QC statuses that will pass or fail them based on metrics of their outputs
Added the ability to for Lanes in a Run, FASTQs, and Analyses, leave Comments when doing so; added ability to view comments
Added the ability to request for Biosamples, Libraries, and Pools
Added the ability to Cancel Requeues for Biosamples, Libraries, and Pools
Added the ability to to different Projects
Added the ability to
Added the ability to
Added the ability to change a , where data from automatic analyses are stored
New Automation
Added a new v2 version of the REST API for the new entities. The v1 API is still completely supported too.
Added the automatic collection of FASTQ data for the same biosamples put in different runs and lanes
Added the ability to automate app launch through the creation and use of app templates called
Added the ability to set for automatically setting a run lane to passed or failed
Added calculations on sequencing yield for each biosample
Added a status on biosamples to indicate it fell short of its required sequencing yield
Existing Features Updated
Replaced samples with Biosamples on app input forms
Replaced Appresults with Datasets on app input forms
Updated the screen to save FASTQ files as a FASTQ datasets linked to a new biosample, rather than a new sample
Updated the File Import screen to save VCF files as a General dataset, optionally linked to a new Biosample
Updated the global search to support finding Biosamples and Datasets
New Capabilities
FASTQ Generation speed dramatically increased when processing NovaSeq runs by running parallel processes for each flowcell lane
Downloader New Features
Updated the downloader client for Windows to work with new BaseSpace Sequence Hub features
Updated the downloader client for Mac to work with new BaseSpace Sequence Hub features
Improved consistency of automatically generated folder names when downloading runs
Improved notifications about download status
Added support for downloading using a proxy server
Added capability to download datasets from the Biosample details Datasets tab
Downloader Bugs Fixed
Fixed an issue that could prevent download of SAV data from NovaSeq Runs (fix requires that new BaseSpace Sequence Hub features are enabled for account)
Fixed an issue where a file that exceeded available disk space was still allowed do be downloaded
Fixed an issue in the the Mac downloader client where the progress bar for queued downloads appeared to show they had already completed
Known Issues
In rare cases, app launch may create a duplicate set of output files for the same appsession. In the case of FASTQ Generation, this produces an additional FASTQ dataset. BaseSpace Sequence Hub prevents subsequent app launches with the related Biosample in these cases. If this occurs, check the Biosample datasets tab for duplicates, and QC fail one set of duplicates.
In some cases, the Run button in app error messages does not launch the app. The app can be launched manually from the GUI.
Sample IDs with the same name are aggregated to a single Biosample of the same name. enables merging of the same sample run across multiple flow cells for downstream processing, however this may result in inaccurate app results if data from different samples with the same sample ID are aggregated to a biosample in error. To prevent unintended aggregation, use unique sample names across all runs. If BaseSpace Sequence Hub detects aggregation upon launching an app, the biosample is locked and must be reviewed and manually unlocked to allow it to proceed with app launch.
Selecting biosamples from the biosamples list before launching an app will not carry over the selected biosamples in to the app form. Instead, re-select the biosamples on the app launch page.
If you get certain biosample related warning triangles when launching an app from the New mode launch page, the normal behavior of being able to override and launch anyway may not work, preventing launching of the app. If this occurs, switch to Classic mode and launch from the corresponding samples.
Features
Began phased rollout of a new feature that will, under some conditions, automatically re-launch apps that have failed
Updating the status of a library now updates the yield on the associated biosample
Demultiplexing information is now displayed only after a run is complete
Bugs Fixed
Fixed issue with incorrect total count of items in appsession properties API
Fixed a rare issue that could cause sequencing statistics in Run Monitoring to be unavailable until run completion for some instruments
Bugs Fixed:
Fixed issue with deleting completed analyses through the API
Fixed issue where the workgroup settings overview page was not displaying some information
Fixed text alignment in project delete confirmation modal
FASTQ Generation
Updated bcl2fastq to 2.20
New Features:
Added support for future NovaSeq flow cell releases
Features
The selected biosamples on app input forms are linked to their respective biosample datasets tab
Project and run sub-tabs have been moved from the side to the top of the panel
The period for downloading detailed usage reports has been increased
Bugs Fixed
Fixed drag and drop issue when importing files into a project
Fixed issue with Regenerate FASTQ launching two duplicate appsessions
Bug Fixes:
Fixed an issue that could cause FASTQ Generation to hang indefinitely with a small number of runs
Improved the robustness of FASTQ Generation when processing NovaSeq data that contains corrupted CBCL files
Fixed issue with Run SAV download packages adding logs and thumbnail files
Fixed issue with backslash character in project, analysis, or dataset name causing extra folder directory to be created during download
Fixed an issue where the Downloader was not working on Enterprise tier accounts.
Fixed a bug preventing users from previewing report and summary report changes during app development.
Fixed an issue where preview search results were not appearing on the Global Search page.
Bugs Fixed:
Fixed an issue where the Downloader tool was not launching in Enterprise tier accounts.
Updated the storage usage to display the amount of storage owned by the user
Bugs Fixed:
Fixed issue preventing users from accessing their BaseSpace Sequence Hub subscription
Fixed issue that allowed the original owner of a transferred project to still see the project's original analysis list
Native apps - Improved the stability of file downloads
Fixed issue where third party app purchases weren't appearing in usage reports.
Fixed issue where files that failed to upload were included in search results.
FASTQ AppSessions can now be generated from the Run Details Summary page
Added requirement to accept EULA for native apps when manually launching in the GUI
###Release 4.17.1 - February 9, 2017
Bugs Fixed
Improved response time for retrieving large files from the Runs page
Discontinued email notifications for accepted app EULAs
Features:
Users are now automatically logged into their last-used workgroup at log in
The active user running an app is tracked in the detailed usage download file
Improved load time performance of the header
Bugs Fixed:
User interface fix to automatically navigate to the top of new table pages
###Release 4.21.1 - April 4, 2017
BaseSpace Sequence Hub
Native app engine security update
FASTQ Generation
Bugs Fixed:
Fixed an issue with FASTQ Generation where reads designed to be shorter than 35 bases were masked out with "N" characters
Features:
Run Monitoring support for NovaSeq instruments
SureCell WTA 3' kit support in Prep Tab
Updated Usage Report (*.csv) file to separate storage and compute costs
Bugs Fixed:
Improved validation of user email addresses
###Release 4.18.1 - February 27, 2017
Bugs Fixed:
Fixed Contact Us and Feedback links within BaseSpace to email Illumina Technical Support
Fixed issue within BaseSpace EU that prevented administrators from granting user access to their Enterprise domain
Features:
Users must now accept EULA for each native app on the website before launching that app via the API
Added Dashboard notification cards to track promotional iCredit balances
Added interactive tutorials to the help menu
Bugs Fixed:
Fixed issue where system logs workgroup name instead of individual's name
###Release 4.19.1 - March 13, 2017
FASTQ Generation Updated:
Updated bcl2fastq to 2.19
Added support for NovaSeq 5000/6000
Features
Added prompt to switch to the correct workgroup context for the run when opening a run owned by a different workgroup.
Added more security to the bulk biosample import API when scheduling analysis workflows.
Updated look of app input form.
Bugs Fixed
Fixed issue with the v1 appsession API showing v2 properties and vice versa.
Fixed issue with run requeues reaching the maximum number of retries after running multi-node Generate FASTQ.
Features:
Improved search and search indexing performance and reliability.
Improved layout of information on the project details page.
Bugs Fixed:
Fixed issue preventing users from previewing report and summary report changes during app development.
Fixed a search issue affecting the TruSight Tumor 170 + Watson for Genomics Converter app.
FASTQ Generation
Updated bcl2fastq to 2.19.1
Bugs Fixed:
Fixed an issue where a small percentage of NextSeq and MiniSeq runs were incorrectly processed such that total number of FASTQ reads generated was reduced (ie, effective yield was reduced).
Features:
Automated email notices are now sent to Basic account users when their storage usage is near or above the limit
The support email link was updated to basespace-support.illumina.com
Bugs Fixed:
Fixed issue where indexing QC information wasn't appearing on some Run Details pages
Fixed issue where the Y-axis of charts in Run Monitoring did not update when "Fix Scale" was checked but a different chart type was selected
Features:
The Analysis Report for an AppResult no longer appears when the AppResult is in the trash
Bugs Fixed:
Fixed an issue where file sizes in trash were misreported as 0 bytes
Fixed issue with misaligned search filter drop-down menu options
Developer Portal
Bugs Fixed:
Fixed issue with errors seen when simulating an app launch
Improved app stability by eliminating several bugs causing rare failures
Fixed issue with the run name being shown twice on the Run Summary page.
Fixed issue with the Generate FASTQ appsession being set to 'QC Failed' when one the FASTQ datasets it produced was manually set to 'QC Failed'.
Fixed issue with Charts on the Runs page sometimes not being shown after .bcl files for a run were deleted.
Fixed issue with the dashboard page not refreshing after accepting a shared or transferred run.
Illumina is notifying affected users so that they can requeue the appropriate runs if desired.
Requeue using the updated version to restore the missing reads.
Fixed an issue where the FastqSummaryF1L# stats file could incorrectly assign non-PF clusters to the non-PF pool for a sample, rather than to the non-PF pool of Undetermined reads.
Fixed issue where a private domain user could share by link to a public domain user, and vice versa
Fixed issue in which the Privacy Policy link on app details screen did not work
Added a new API to reschedule an existing automated analysis.
Changed the Tumor Normal workflow to send analysis output to the default project associated with the tumor biosample instead of the default project associated with the normal biosample.
Bugs Fixed
Added support to automatically append a number to a transferred project when a project with the same name already exists in the account that received the project.
Added pagination to the Public Data page to allow display of all public data when the number of items exceeds the page limit.
Known Issues
Apps using dataset file choosers or dataset choosers containing optional display fields are currently not functioning correctly and have been disabled until fixed.
Improvements to bill details page
Update to App Results page to show compute charges to two decimal places
Improved Launch App dropdown menu response time
Warn users if there are operations in progress when they empty the trash
Added email notification for apps that aborted due to error
Bug fixes:
Fixed issue that prevented removing of collaborators from the Share dialog
Fixed issue within the Developer Portal that truncated the Preview section
Fixed issue that limited the number of Workgroups listed within the Workgroup menu
Fixed issue that allowed users to move data in a pending transfer state to trash. User now needs to cancel transfer prior to move.
Significant back-end database changes to support scaling for future growth
Bugs Fixed:
Fixed issue with trash size sum not updating after items were restored or emptied
Fixed issue with being able to delete projects and their samples at the same time, causing issues with emptying trash
Fixed issue with file count not updating on run details page after a files-only delete of the run
###Release 4.16.1 - January 31, 2017
Bugs Fixed:
Fixed issue with high database CPU usage
###Release 4.16.2 - February 1, 2017
Bugs Fixed:
Fixed issue with Indexing QC information not appearing after a run
###Release 4.16.3 - February 2, 2017
Bugs Fixed:
Performance fix for run uploads impacting server responsiveness
FASTQ Generation Updated:
Updated bcl2fastq to 2.18
Support for Universal Molecular Indicators (UMIs) addition to FASTQ files when used with the SureCell WTA 3' library prep kit
Improved app stability by eliminating several bugs causing rare failures
Fixed an issue causing BaseSpace Sequence Hub Indexing QC Metrics page to display index 1 and index 2 in the same column, rather than in separate columns as expected
Fixed an issue with read numbering in the ConversionStats.xml output file
Updated app details pages to include screenshots and expandable text descriptions
Updated developer agreements
Bugs Fixed
Fixed a permissions issue that prevented workgroup users from launching an app
Fixed issue in which the Prep Tab pooling page did not highlight the selected samples
Fixed file chooser table display for Firefox browsers
Bugs Fixed
Fixed issue with some apps aborting on startup
Features
Added developer portal support for collaborative app development within your BaseSpace Sequence Hub workgroup
Added a featured apps section to the apps page
Bugs Fixed
Fixed issue with action toolbar incorrectly displaying on run summary page
Fixed decimal places of compute cost on app details page
FASTQ Generation - Staged Roll Out Complete
Fixed an issue that could cause FASTQ Generation to hang on NextSeq and MiniSeq runs
Bugs Fixed
Fixed issue with Cufflinks app reports not showing up for some users