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COVFlow: phylodynamics analyses of viruses from selected SARS-CoV-2 genome sequencesuse asterix (*) to get italics
Gonché Danesh, Corentin Boennec, Laura Verdurme, Mathilde Roussel, Sabine Trombert-Paolantoni, Benoit Visseaux, Stephanie Haim-Boukobza, Samuel AlizonPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"
<p style="text-align: justify;">Phylodynamic analyses generate important and timely data to optimise public health response to SARS-CoV-2 outbreaks and epidemics. However, their implementation is hampered by the massive amount of sequence data and the difficulty to parameterise dedicated software packages. We introduce the COVFlow pipeline, accessible at <a href="" target="_blank" rel="noopener"></a>, which allows a user to select sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID) database according to user-specified criteria, to perform basic phylogenetic analyses, and to produce an XML file to be run in the Beast2 software package. We illustrate the potential of this tool by studying two sets of sequences from the Delta variant in two French regions. This pipeline can facilitate the use of virus sequence data at the local level, for instance, to track the dynamics of a particular lineage or variant in a region of interest.</p> should fill this box only if you chose 'All or part of the results presented in this preprint are based on data'. URL must start with http:// or https:// should fill this box only if you chose 'Scripts were used to obtain or analyze the results'. URL must start with http:// or https:// should fill this box only if you chose 'Codes have been used in this study'. URL must start with http:// or https://
COVID-19, molecular epidemiology, sequence database, phylogenetics, public health
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Bioinformatics, Evolutionary genomics
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2022-12-12 09:04:01
Emmanuelle Lerat