A Nextflow pipeline for T-cell receptor repertoire reconstruction and analysis from RNA sequencing data

T-cell receptor (TCR) analysis is relevant for the study of immune system diseases. The expression of TCRs is usually measured with targeted sequencing approaches where TCR genes are selectively amplified. However, many non-targeted RNA-seq experiments also contain reads of TCR genes, which could be leveraged for TCR expression analysis while reducing sample requirements and costs. Moreover, a step-by-step pipeline for the processing of transcriptome RNA-seq reads to deliver immune repertoire data is missing, and these types of analyses are usually not included in RNA-seq studies of immunological conditions. This represents a missed opportunity for complementing them with the analysis of the immune repertoire.