VIPERA

A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis.

Viral mutations within patients nurture the adaptive potential of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during chronic infections, which are a potential source of variants of concern. Viral Intra-Patient Evolution Reporting and Analysis (VIPERA) is a user-friendly workflow to easily identify and study within-host evolution in SARS-CoV-2 serially sampled infections. First, it provides an aggregate of population genomics and phylogenetic analyses that allows researchers to determine if a collection of SARS-CoV-2 samples originates from a single-virus, serially sampled infection. Then, it provides insights into intra-host evolutionary dynamics, tracking variant trajectories and selective pressure over time. These results are automatically packed in an HTML report that serves as a guide for prioritizing and refining subsequent analyses using the newly generated data for downstream studies.