New FASTQ Generation App on BaseSpace

As part of the latest release of BaseSpace, we are pleased to announce an update to the FASTQ generation process that will provide a faster, richer experience for HiSeq and NextSeq users.


Our new FASTQ Generation tool provides two new major benefits:

  • Changes to the BCL to FASTQ conversion will increase speed dramatically, up to 10X faster in some cases.
  • FASTQ Generation sessions can now be viewed on the Dashboard and Analyses lists. This allows you to view logs and result details, making it easier to evaluate any issues.

FastQ Gen2

The new FASTQ Generation process is an implementation of the algorithms used in the BCL2FASTQ 2.17 RPM in BaseSpace.  FASTQ files will continue to be generated automatically and you’ll be able to use this data with all of our apps.

We hope you enjoy these changes.  We also released a few other minor updates – for more information please review the BaseSpace 3.23.0 Release Notes.

We’re always looking for ways to improve your BaseSpace experience and welcome any feedback or suggestions.


  1. We just had a NextSeq run ‘fail’ with your new workflow with this error: “Invalid characters in project: our-project name Only alphanumeric, ‘-‘, or ‘_’ characters are allowed.”

    This is our 4rd run, 3 other runs on our new NextSeq500 completed fine and fastq files were generated. How can we get in touch with tech support to see if the bcl file still resides on BaseSpace and if it can be recovered.

  2. Following the upgrade reported here our application started getting permission errors.

    ServerResponseException: ‘Error with API server response: BASESPACE.COMMON.INSUFFICIENT_RESOURCE_PERMISSIONS: Sorry but this requires WRITE access to this AppSession resource.’

    Does anyone know if the software upgrade caused this?

    We are not clear from the docs how change access permissions for tokens etc. The web documentation has some sample urls, but some appear to be incorrect.

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