Auto-Launch with FASTQs generated by Standalone BCL Convert Pipeline (Start from FASTQ)

When using BSSH Run Planning to generate a sample sheet to auto-launch analysis on ICA, you must designate "Start from Fastq" to be True or False (default is False). If you choose "False", BSSH will kick off the TSO 500 pipeline normally using BCL input from the run folder.

If you choose "True" for this option, BSSH will run two ICA pipelines in sequence:

• First, it will run the BCL Convert v3.10.9 pipeline to generate the FASTQ files

• Second, it will kick off the TSO 500 pipeline using the FASTQ files generated above as the input

Please note. Run QC metrics are generated inside the TSO 500 pipeline from interop files in the run folder. When starting TSO 500 from FASTQ (via auto-launch or manual launch), Run QC metrics will not be generated.

When the auto-launched analysis completed, you will see the analysis result shows results from both the BCL Convert pipeline and the TSO 500 pipeline, like below: