July 10, 2015 - 3.20.4 - Application Purchase Update

Bug Fixes

• Application pricing restored for published apps

• Developer site now retains test user order on details page

• Developer site warns about unsaved changes

December 11, 2015 - 3.23.2 - Bug Fix and Input Form Update

• Features:

  • Developers may now configure their web applications to bypass the input form

• Bug Fixes:

  • Fixed an issue related to using access tokens when accessing files in the Projects and AppSessions APIs

December 03, 2015 - 3.23.0 - Issues

As part of the latest release of BaseSpace, we have identified a few bugs as follows:

1. Projects with any character other than alphanumeric, underscore (_), or dash (-), will cause BCL2FASTQ 2.17 to fail. Since the latest BaseSpace release is using the same core algorithms, FASTQ Generation will fail if invalid characters are used. Users will see an error notification, and the log file will have details on the error.

   • As a temporary workaround: Users can remove the invalid characters OR make sure the column header in the SampleSheet Data section is called SampleProject NOT Sample_Project OR SAMPLE_PROJECT. PrepTab users with NextSeq will need to rename their Projects for the time being. Users will need to manually move Samples to existing Projects from newly created Projects.

2. For samples that have an underscore (_) in the name, the automatic conversion to a dash (-) in the file name, as occurred previously, is not occurring. As a result, a some apps may fail to launch.

   • A workaround for the time being is to rename the sample without the underscore, and requeue the FASTQ generation.

3. IGV is not opening projects and samples, because a BaseSpace API is failing.

We are working towards providing a fix for all of these as soon as possible.

June 25, 2015 - 3.20.0 - Versioning of Apps

• Features:

  • Storage Metering

  • Application Versioning

• Updates:

  • Application Description Page Redesign

  • Developer Portal Redesign

Storage Metering

• Users can now view overall storage information under My Account

Application Versioning

• Multiple versions of applications in BaseSpace are now grouped together in a single location

• New What's New section added to each version of an application, this section indicates any announcements for this application

• New Release Notes section added to each version of an application, this section will include the latest updates included in this version of the application from the previous version

July 3, 2015 - 3.20.3 - Versioning Update

Bug Fixes

• Viewing results from unpublished applications

• Dynamically updated app forms getting 403 on callback

April 11, 2015 - 3.17.0 - Download Experience

New Features

Download Experience: Added new download dialog on run details and analysis details pages. Run details dialog allows download of all fastq files that were produced that you have access to. The analysis details allows filtering by all, BAM, and VCF.

Run Transfer: Failed runs can now be transferred to another owner.

December 01, 2015 - 3.23.0 - FASTQ Generation and Run UI Updates

• New FASTQ Generation App v1.0.0 in BaseSpace (see below for more details)

• Updates to the Run details page

• Bug Fixes:

  • Fixed import and export bugs related to Windows 10

  • Fix for incorrect search results being returned

  • Fixed an issue related to sharing data that resulted in conflicts

FASTQ Generation App v1.0.0

• Up to 10x overall speed improvement

• Improved robustness, more common in larger volume datasets

• All FASTQ workflows on the Runs List page have been renamed Generate FASTQ. We will not be reprocessing old Runs, just adjusting the name

• AppSessions/Analyses for the app are now visible in the Analysis section of your Projects

  • FASTQ Generation now has a new icon (above)

  • Includes log files and all input information

  • After the app completes, the Log Files link on the Analysis page will contain key files such as DemuxSummary, Sample Sheet Used, and Adapter Trimming

  • Known limitation: Sample sheet is a string of text

• The Legacy App (old version of FASTQ Generation) is called BaseSpace FastQ v1.0.0 and the new App is called FASTQ Generation v1.0.0

• MiSeq Runs will still use the MSR FASTQ Generation workflow (the mechanism to requeue FASTQ Generation has not changed)

• FASTQ Generation is now a BaseSpace Native App

May 21, 2015 - 3.19.0 - SAV Update

SAV Charts Overhaul

• Pan And Zoom of Charts (Data by Cycle, Data by Lane, QScore)

• Ability to "Fix Scale" of graphs to allow for apples-to-apples comparison for cycles and allow for trend-spotting.

• Enhancements to "Run Summary" stats tables

• Improved reporting of Demultiplex results

• Overall speed improvements

• As always, most of this data is available via our API, for example the "NextSeq-500-V2-Nextera-XT-384-plex-E-Coli" , you can see stats with these API calls:

Blog Post:

April 08, 2015 - 3.16.2 - App Launch API

New Features

• App Launch API: Added new POST: applications/{id}/appsessions endpoint to allow launching of Native Apps using the BaseSpace Rest API. More information is available in the

• API Rate Limitations: Added rate limitations to the API, described in more detail

• LaunchSpace: Set of python scripts released by the BaseSpace team to allow BaseSpace users to automatically launch analysis on their samples as soon as they are ready. LaunchSpace is described in more detail in its

• Added Python SDK guide for launching Native Apps on your data, available in the

April 17, 2015 - 3.17.1 - Minor API Update

Minor API Update

• Updated the users/{id}/runs API endpoint to now return any Runs in BaseSpace that were Locked during sequencing

March 03, 2015 - 3.15.1 - NeoPrep Support

New Features

• NeoPrep now supports pooling of libraries produced from the NeoPrep instrument. (Instrument Owners Only)

- New HelpCenter is now default help link. The HelpCenter is a newly designed support site with an increasing amount of new articles and tutorials. See more [here](https://help.basespace.illumina.com "BaseSpace HelpCenter")

Bug Fixes

• External html links can no longer be included in share comments

December 09, 2015 - 3.23.1 - FASTQ Generation Name Verification and IGV Fixes

• Bug Fixes:

  • Fixed issue preventing IGV from loading analyses to view

  • Give better warnings for invalid samplesheets that have unsupported characters

  • Performance improvements for sample details

  • Resolved issues launching RNAExpress 1.0

• Notes:

  • The FASTQ generation application does not support some characters in a Project name. Please limit the characters you use in project names to alphanumeric, dashes, and underscores where possible.

May 27, 2015 - 3.19.1 - Minor SAV Update

Minor SAV Update

• This release contains a performance improvement for the Runs charts in BaseSpace

May 7, 2015 - 3.18.0 - Native App Job Scheduling Update

Native App Job Scheduling Update

• Significant improvements to the job scheduler for all Native applications in BaseSpace

March 13, 2015 - 3.15.2 - Email Fixes

Bug Fixes

• Run and Analysis Completed Emails No longer filtered

• Updated Styling for header on FAQ, Public Data, and Agreements.

• 3.23.2

• 3.23.1

• 3.23.0 Issues

• 3.23.0

• 3.20.4

• 3.20.3

• 3.20.0

• 3.19.1

• 3.19.0

• 3.18.0

• 3.17.1

• 3.17.0

• 3.16.2

• 3.16.0

• 3.15.2

• 3.15.1

March 30, 2015 - 3.16.0 - MSR conversion

New Features

• MSR conversion: MSR v2.4.60.8 with the new look of reports. Reports for the last two supported MSR versions are re-generated.

• BGZipped FASTQs can now be uploaded in web upload tool.

• Supports bcl2fastq latest release.

Example screenshots: