Advanced Topics

Demultiplex only option

In order to break up the workflow, one may wish to run the software with the demux only option. The pipeline will perform FASTQ generation with the settings provided by default or as specified in the sample sheet. Then the subsequent analysis may start from FASTQ.

CRAM input

When CRAM is used as input, the reference genome used to generate the CRAM files is required. This may be provided using the custom configuration file