theosanderson / molnupiravir

Data and scripts used in "Identification of a molnupiravir-associated mutational signature in SARS-CoV-2 sequencing databases".

mutational_spectra directory

• Spectra from long phylogenetic branches, processed using MutTui
• Spectra from AGILE trial, processed using MutTui

alteri_et_al_processing

• Scripts used to process data from Alteri et al.
• Alteri et al. spectra

r_notebook

• R notebook producing all figures and analyses in the paper

archive

Older scripts

bte

Used to extract data from MAT for subsequent processing

open_data_version

A version of the analysis using open data from INSDC for reproducibility

nextclade_version

A version of the analysis using Nextclade for reproducibility of full 15-million sequence results without an UShER tree

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Exact package versions for the R environment we used are here. Our work was carried out on macOS 13.0

molnupiravir's Issues

how to generate the `refs_results/*.tsv` files?

Dear @theosanderson,

Could I know how to generate the refs_results/*.tsv files? Thanks.