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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"
2023
<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="https://gitlab.in2p3.fr/ete/CoV-flow" target="_blank" rel="noopener">https://gitlab.in2p3.fr/ete/CoV-flow</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>
https://gisaid.org/You 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://
https://gitlab.in2p3.fr/ete/CoV-flow/scriptsYou should fill this box only if you chose 'Scripts were used to obtain or analyze the results'. URL must start with http:// or https://
https://zenodo.org/record/8016623You 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
NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).
Bioinformatics, Evolutionary genomics
No need for them to be recommenders of PCI Genomics. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct
e.g. John Doe [john@doe.com]
2022-12-12 09:04:01
Emmanuelle Lerat