A comprehensive benchmarking study of adaptive immune receptor repertoire sequencing data aligners

Abstract

Aim. The reliability of Adaptive Immune Receptor Repertoire sequencing (AIRR–Seq) data analysis hinges on the performance of alignment tools, but due to frequent inconsistency in output formats and user experience, an objective comparison of AIRR data aligners is still missing. Thus, here we aimed to benchmark the most widely used AIRR–Seq data analysis tools – HighV–Quest, IgBlast, and MiXCR – and evaluate their alignment accuracy [1, 2]. Conclusions. Our study shows that based on the V–region overlap call, IgBlast achieves the best performance, with HighV–Quest and MiXCR following respectively. We also demonstrate that the distribution of V–region genes in reads has no statistically significant effect on the mapping outcome of each read.