Streamlining T-cell receptor based research by combining competitve tools in nf-core/airrflow

Streamlining T-cell Receptor based immunological research by combining competitve state-of-the-art tools in nf-core/airrflow The immune system recognizes antigens from external sources such as viruses, bacteria, or cancers, and initiates an immune response that is carrying out the required action. T-cells, one the major players in adaptive immunity either eliminate infected cells or release cytokines to invoke a response from other immune cells. Each person has a unique T-cell repertoire comprising numerous clonal groups (10^6-10^8), each with a distinct T-cell receptor (TCR). Gabernet et al. demonstrated the effectiveness of the analysis of a B-cell receptor (BCR) repertoire study using nf-core/airrflow, a containerized and publicly accessible computational pipeline within the nf-core community which can be used to study the adaptive immune receptor repertoire (AIRR). The pipeline already incorporates state-of-the-art tools such as the Immcantation framework while ensuring portability, reproducibility, scalability, and adherence to the FAIR principles. We present the innovations with a focus on the T-cell component of nf-core/airrflow by incorporating new functionalities for analyzing both publicly available and newly generated TCR-sequencing data as well as raw single-cell AIRR-sequencing data and for extracting AIRR sequences from raw unselected RNA-seq data. This is possible through incorporation of MiXCR, TRUST4 and the cellranger vdj frameworks into the pipeline. Furthermore, these tools have been smoothly integrated with the downstream Immcantation framework by the use of the AIRR community standard format, enabling users to leverage and combine the strengths of different tools in a single pipeline run and to compare the results from various competing tools. Consequently, this approach can enhance the accuracy and significance of TCR repertoire sequencing experiments by expanding the tool repertoire of nf-core/airrflow to enable comparative analysis of results across tools.