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Published on: August 14, 2018
RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis
Alexander G Lucaci1, Jordan D Zehr1, Stephen D Shank1
1Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, USA.
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.
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