TRAPeS

TRAPeS (TCR Reconstruction Algorithm for Paired-End Single-cell) addresses the link between T cell receptor (TCR) diversity and T cell state heterogeneity, which is crucial for effective immunity. Current methods for inferring TCR sequences from single-cell RNA-sequencing (scRNA-seq) are limited in sensitivity and require long sequencing reads, impacting cost and feasibility. 'TRAPeS' is introduced as a publicly available tool that efficiently extracts TCR sequence information from short-read scRNA-seq libraries. It demonstrates accuracy and superior sensitivity compared to existing methods. Applying 'TRAPeS' to analyze CD8+ T cell responses in humans and mice, the tool couples TCR analysis with transcriptome examination. In the context of CD8+ T cells specific to Yellow Fever Virus (YFV), the study reveals that the 'naive-like' memory population possesses distinct TCR characteristics, indicating an association between TCR usage and differentiation states in the CD8+ T cell response to YFV.