Question: Are the mkfastq pipelines interchangeable between products?
Answer: Each mkfastq wrapper populates the product and assay version-specific parameters for the MAKE_FASTQ_CS pipeline invocation. For example, Long Ranger and Supernova are based on Chromium Genome assay data, and so the mkfastq pipeline is the same for both. Meanwhile, Cell Ranger is used to process Chromium Single Cell 3' v1, 3' v2, and 5' Gene Expression and V(D)J assay data.
Thus, cellranger mkfastq and spaceranger mkfastq are different as the former will not be able to deal with Visium dual index sets; cellranger mkfastq and cellranger-dna mkfastq are different; cellranger mkfastq and longranger
mkfastq are not compatible; longranger mkfastq and supernova mkfastq are same.
Thus it is advised to use the version of mkfastq that matches the pipeline that you are planning to run.
For more information on the parameters passed by mkfastq to bcl2fastq please see What bcl2fastq parameters does mkfastq use internally? If you prefer not to use mkfastq, we recommend demultiplexing with bcl2fastq directly.