The nf-core/bcellmagic pipeline is built to analyze B-cell repertoire sequencing data. It makes use of the Immcantation 2.5.0 toolset and requires targeted sequencing data of the V, D, J and C regions of the B-cell receptor (primers for the V and C genes).

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.


The nf-core/bcellmagic pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation
  2. Pipeline configuration
  3. Running the pipeline
  4. Output and how to interpret the results
  5. Troubleshooting


nf-core/bcellmagic was originally written by Gisela Gabernet, Simon Heumos, Alexander Peltzer.