VAPPER

VAPPER (Variant Antigen Profiler) is a software tool that automates the analysis of variant surface glycoprotein repertoires in African trypanosomes, specifically the livestock pathogens Trypanosoma congolense and Trypanosoma vivax. These parasites possess hundreds of highly variable variant antigen genes, making their analysis challenging for traditional read mapping and variant calling methods.

VAPPER overcomes this difficulty by generating variant antigen profiles from genomic and transcriptomic sequencing data, allowing for large-scale comparative analysis of these gene families across different isolates. The tool produces publication-ready figures that compare the queried isolate with a database of existing strains. VAPPER is implemented in Python and can be installed on a local Galaxy instance or a Linux platform. It is the first tool to enable high-throughput analysis of African trypanosome variant antigens.