Bioinformatics analysis of SARS-CoV-2 origins

Motivation

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Collaborators

• Jacques van Helden (ORCID 0000-0002-8799-8584)
• Etienne Decroly (ORCID 0000-0002-6046-024X)
• Erwan Sallard (erwan.sallard@ens.psl.eu)
• Didier Casane (http://www.egce.cnrs-gif.fr/?p=1289)
• José Halloy (ORCID 0000-0003-1555-2484)

Access

• Web pages: https://jvanheld.github.io/SARS-CoV-2_origins/
• Git repository: https://github.com/jvanheld/SARS-CoV-2_origins

Introduction

This repostiroy contains the code and data enabling to reproduce the results of our genoic and phylogentic analysis of SARS-CoV-2 origins, published in a French journal in August 2020, and whose English translation was published in Environmental Chemistry Letters in February 2021.

• E. Sallard, J. Halloy, D. Casane, J. van Helden, É. Decroly, Retrouver les origines du SARS-CoV-2 dans les phylogénies de coronavirus, Med Sci (Paris). 36 (2020) 783–796. https://doi.org/10.1051/medsci/2020123.

• E. Sallard, J. Halloy, D. Casane, E. Decroly, J. van Helden, Tracing the origins of SARS-COV-2 in coronavirus phylogenies: a review, Environ Chem Lett. (2021). https://doi.org/10.1007/s10311-020-01151-1.

Files

Contents	Type	doc
Installation and usage	manual	INSTALL-and-USE.md
Full-genome PIP profiles	report	[html] [Rmd source]
PIP profiles of genomic features (1-to-n matches)	report	[~20 strains] [~40 strains] [~60 strains] [Rmd source]
PIP profiles of spike protein sequences	report	[~20 strains] [~40 strains] [~60 strains] [Rmd source]
Phylogeny inference	report	[html] [Rmd source]