Thumbnail Image
Item

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

; ; ; 
Bouvier, Dave
; 
Mei, Han
; 
Nekrutenko, Anton
; 
Martin, Darren P.
; 
Citations
Altmetric:
Genre
Pre-print
Date
2022-01-18
Advisor
Committee member
Group
Institute for Genomics and Evolutionary Medicine
Department
Subject
Permanent link to this record
http://hdl.handle.net/20.500.12613/7570
Collections
COVID-19 Research
Show all metadata
Files
Thumbnail Image
LucaciEtAl-Preprint-2022.pdf
Adobe PDF, 346.29 KB
Research Projects
Organizational Units
Journal Issue
DOI
https://doi.org/10.1101/2022.01.15.476448
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.
Description
Citation
Citation to related work
bioRxiv
Has part
ADA compliance
For Americans with Disabilities Act (ADA) accommodation, including help with reading this content, please contact scholarshare@temple.edu
Embedded videos
License
Attribution CC BY
cb