Deep mutational scanning of SARS-CoV-2 Omicron BA.2 spike and mapping of escape mutations for COV2-2130 and its derivate antibody¶
This page documents the data analysis. For the actual code, see https://github.com/dms-vep/SARS-CoV-2_Omicron_BA.2_spike_DMS_COV2-2130
Study by Bernadeta Dadonaite and Jesse Bloom.
Workflow¶
Below is the rulegraph for the snakemake workflow.
Click here
for the more detailed filegraph.
Analysis notebooks¶
Many of the plots in these notebooks are interactive, so try mousing over points for details, using dropdowns, etc.
- Analyze PacBio CCSs
- Build PacBio consensus sequences
- Build the codon variants
- Functional scores of variants for viral entry
- Fit global epistasis models
- Functional effects of mutations across replicates
- Counts of variants
- Probabilities of escape and neutralization in antibody selections
- Fit
polyclonal
models - Antibody-escape averaged across replicates
- Compare antibody neutralization values