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bioRxiv · 10.1101/2022.01.15.476448

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

Lucaci, A. G.·Zehr, J. D.·Shank, S. D.·Bouvier, D.·Mei, H.·Nekrutenko, A.·Martin, D. P.·Pond, S.
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Abstract

An important component of efforts to manage the ongoing COVID19 pandemic is the Rapid Assessment of how natural selection contributes to the emergence and proliferation of potentially dangerous SARS-CoV-2 lineages and CLades (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. AvailabilityRASCL 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. ContactDr. Sergei L Kosakovsky Pond (spond@temple.edu). Supplementary informationN/A

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Lucaci, A. G., Zehr, J. D., Shank, S. D., Bouvier, D., Mei, H., Nekrutenko, A., Martin, D. P., Pond, S.. 2022-01-18. RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis. https://doi.org/10.1101/2022.01.15.476448

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