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

ABSTRACT

An important component of efforts to manage the ongoing COVID19 pandemic is the R apid A ssessment of how natural selection contributes to the emergence and proliferation of potentially dangerous S ARS-CoV-2 lineages and CL 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. AVAILABILITY: RASCL is available from a dedicated repository at https//github.com/veg/RASCL and as a Galaxy workflow https//usegalaxy.eu/u/hyphy/w/rascl . Existing clade/variant analysis results are available here https//observablehq.com/@aglucaci/rascl . CONTACT Dr. Sergei L Kosakovsky Pond ( spond@temple.edu ). SUPPLEMENTARY INFORMATION N/A.