bcRflow: a Nextflow pipeline for characterizing B cell receptor repertoires from non-targeted transcriptomic data

Area of Science:

• Immunology
• Bioinformatics
• Computational Biology

Background:

• B cells are crucial for adaptive immunity, generating diverse B cell receptors (BCRs) to recognize foreign antigens.
• Targeted immune sequencing for BCR profiling is costly and requires specific tissue samples.
• Analyzing non-targeted transcriptomics data offers a cost-effective alternative for BCR repertoire profiling, but lacks standardized pipelines.

Purpose of the Study:

• To introduce bcRflow, a Nextflow pipeline for characterizing B cell receptor repertoires from non-targeted transcriptomics data.
• To provide a comprehensive, reproducible, and scalable solution for immune repertoire extraction and analysis.
• To facilitate deeper insights into B cell immune responses for biological and clinical applications.

Main Methods:

• Development of bcRflow, a Nextflow pipeline with modules for alignment, processing, and visualization of BCR repertoires.
• Implementation of nf-core configurations for enhanced portability and accessibility across various computing environments (HPC, cloud, local).
• Analysis of a public dataset of bulk transcriptomic samples from COVID-19 patients and healthy controls to demonstrate pipeline functionality.

Main Results:

• bcRflow successfully characterizes BCR repertoires from non-targeted transcriptomics data.
• The pipeline demonstrated its ability to provide valuable insights into B cell immune responses.
• The analysis of COVID-19 patient data showcased the pipeline's utility in a relevant biological context.

Conclusions:

• bcRflow streamlines the analysis of BCR repertoires from non-targeted transcriptomics data.
• The pipeline offers a scalable, reproducible, and accessible tool for researchers.
• bcRflow enhances the study of B cell immune responses in biological and clinical research.