5.6.0

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.