B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
Define where the pipeline should find input data and save output data.
Experimental protocol used to generate the data
Define the primer region start and how to deal with the primer alignment.
Define how UMI barcodes should be treated.
Options for adapter trimming and read clipping
Options for the pRESTO sequence assembly processes
Options for the VDJ annotation processes.
Options for bulk sequence filtering after VDJ assignment.
Define how the B-cell clonal trees should be calculated.
Options for the reference genome indices used to align reads.
Parameters used to describe centralised config profiles. These should not be edited.
Set the top limit for requested resources for any single job.
Less common options for the pipeline, typically set in a config file.