@article{Lucaci2022,
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. Availability RASCL is available from a dedicated repository at {\textless}https://github.com/veg/RASCL{\textgreater} and as a Galaxy workflow {\textless}https://usegalaxy.eu/u/hyphy/w/rascl{\textgreater}. Existing clade/variant analysis results are available here: {\textless}https://observablehq.com/@aglucaci/rascl{\textgreater}. Contact Dr. Sergei L Kosakovsky Pond (spond{\{}at{\}}temple.edu). Supplementary information N/A {\#}{\#}{\#} Competing Interest Statement The authors have declared no competing interest.},
author = {Lucaci, Alexander G and Zehr, Jordan D and Shank, Stephen D and Bouvier, Dave and Mei, Han and Nekrutenko, Anton and Martin, Darren P and Pond, Sergei L Kosakovsky},
doi = {10.1101/2022.01.15.476448},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Lucaci et al. - 2022 - RASCL rapid assessment of SARS-CoV-2 clades through molecular sequence analysis.pdf:pdf},
journal = {bioRxiv},
keywords = {OA,genomics{\_}fund{\_}ack,original},
mendeley-tags = {OA,genomics{\_}fund{\_}ack,original},
month = {jan},
pages = {2022.01.15.476448},
pmid = {35075458},
publisher = {Cold Spring Harbor Laboratory},
title = {{RASCL: rapid assessment of SARS-CoV-2 clades through molecular sequence analysis}},
url = {https://www.biorxiv.org/content/10.1101/2022.01.15.476448v1 https://www.biorxiv.org/content/10.1101/2022.01.15.476448v1.abstract},
year = {2022}
}

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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 \\textlesshttps://github.com/veg/RASCL\\textgreater and as a Galaxy workflow \\textlesshttps://usegalaxy.eu/u/hyphy/w/rascl\\textgreater. Existing clade/variant analysis results are available here: \\textlesshttps://observablehq.com/@aglucaci/rascl\\textgreater. Contact Dr. Sergei L Kosakovsky Pond (spond\\at\\temple.edu). 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