summary.md

Summary

Analysis run by Snakefile using this config file. See the README in the top directory for details.

Here is the rule graph of the computational workflow:

Here is the Markdown output of each notebook in the workflow:

1. Get codon-variant-table from here.

2. Count variants and then aggregate counts to create to create variant counts file.

3. Analyze sequencing counts to cells ratio; this prints a list of any samples where this ratio too low. Also creates a CSV with the sequencing counts, number of sorted cells, and ratios for all samples.

4. Escape scores from variant counts.

5. Escape fractions for mutations and homologs; creating mutation escape fraction file and homolog escape fraction file.

6. Call sites of strong escape, and write to a CSV file.

7. Plot escape profiles.

8. Map escape profiles to *.pdb files using this notebook

9. Count mutations in GISAID RBD sequences to create this counts file.

10. Analyze GISAID mutations at sites of escape.

11. Escape from binding by homologs.

12. Make supplementary data files, which are here. These include dms-view input files.