VAPPER: High-throughput Variant Antigen Profiling in African trypanosomes

Abstract

36 37 Background: Analysing variant antigen gene families on a population scale is a 38 difficult challenge for conventional methods of read mapping and variant calling due 39 to the great variability in sequence, copy number and genomic loci. In African 40 trypanosomes, hemoparasites of humans and animals, this is complicated by variant 41 antigen repertoires containing hundreds of genes subject to various degrees of 42 sequence recombination. Findings: We introduce Variant Antigen Profiler 43 (VAPPER), a tool that allows automated analysis of variant antigen repertoires of 44 African trypanosomes. VAPPER produces variant antigen profiles for any isolate of 45 the veterinary pathogens Trypanosoma congolense and Trypanosoma vivax from 46 genomic and transcriptomic sequencing data and delivers publication-ready figures 47 that show how the queried isolate compares with a database of existing strains.

VAPPER: High-throughput variant antigen profiling in African trypanosomes of livestock

“…Snapshots of our code and other data further supporting this work are available in the GigaScience repository, GigaDB [40].…”