SARS-CoV-2 full spike BA.1 library deep mutational scanning validations
In this project we validate SARS-CoV-2 full spike deep muttaional scanning for BA.1 library.
Original BA.1 full spike deep mutational scanning data can be found here.
These scripts preform the following:
- virus_titers_for_mAb_escape.ipynb and virus_titers_functional_mutants.ipynb calculate titers for pseudotyped viruses used either for antibody escape or spike function analysis.
- functional_virus_titer_fold_change.ipynb plots fold chance in virus titers compared to unmutated spike
- spike_neutralization.ipynb runs neutralization analysis for spike mutants against different monoclonal antibodies
- VSVG_neutralization.ipynb runs neutralization analysis for VSV-G or unmutated BA.1 spike pseudotyped lentivirus against different monoclonal antibodies
- Lycov1404_yeast_lenti_dms_comparison.ipynb compares deep mutational scanning data for full spike lentivirus-based DMS and yeast-based RBD DMS.
plasmid_maps subfolder contains plasmid maps for splike and VSV-G expression plasmids used for making pseudoviruses used in performing neutralization ploted in this analysis.
To run the analysis using snakemake pipeline type:
snakemake --cores 1
After the run is finished analysis results are found in results folder.