PANPROVA: pangenomic prokaryotic evolution of full assemblies.

ABSTRACT

MOTIVATION Computational tools for pangenomic analysis have gained increasing interest over the past two decades in various applications such as evolutionary studies and vaccine development. Synthetic benchmarks are essential for the systematic evaluation of their performance. Currently, benchmarking tools represent a genome as a set of genetic sequences and fail to simulate the complete information of the genomes, which is essential for evaluating pangenomic detection between fragmented genomes. RESULTS: We present PANPROVA, a benchmark tool to simulate prokaryotic pangenomic evolution by evolving the complete genomic sequence of an ancestral isolate. In this way, the possibility of operating in the preassembly phase is enabled. Gene set variations, sequence variation and horizontal acquisition from a pool of external genomes are the evolutionary features of the tool. AVAILABILITY AND IMPLEMENTATION PANPROVA is publicly available at https//github.com/InfOmics/PANPROVA. The manuscript explicitelly refers to the github repository. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.