Varaps: a python package for estimating SARS-CoV-2 lineages proportions from pooled sequencing data (ANRS0160)

Wastewater-based epidemiology has been investigated as a very effective way of monitoring SARS-CoV-2 variants. This can be achieved through accurate lineage deconvolution of wastewater sequencing data. Variants Ratios from Pooled Sequencing (VaRaPS) is a Python package designed for this purpose, utilizing pooled sequencing data and lineage mutation profiles to estimate their proportions. VaRaPS re-implements core algorithms from the literature, achieving significant improvements in computational speed and efficiency. Comparative analyzes with simulated and synthetic data sets demonstrate its superior performance in lineage prevalence estimation, underscored by its user-oriented design for broader accessibility. By improving speed and accuracy in SARS-CoV-2 variant analysis, VaRaPS offers valuable insights into viral evolution, supporting ongoing surveillance efforts in the post-pandemic landscape.