RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis

An important component of efforts to manage the ongoing COVID19 pandemic is the <underline>R</underline>apid <underline>A</underline>ssessment of how natural selection contributes to the emergence and proliferation of potentially dangerous <underline>S</underline>ARS-CoV-2 lineages and <underline>CL</underline>ades (RASCL). The RASCL pipeline enables continuous comparative phylogenetics-based selection analyses of rapidly growing clade-focused genome surveillance datasets, such as those produced following the initial detection of potentially dangerous variants. From such datasets RASCL automatically generates down-sampled codon alignments of individual genes/ORFs containing contextualizing background reference sequences, analyzes these with a battery of selection tests, and outputs results as both machine readable JSON files, and interactive notebook-based visualizations.