summary.md

Summary

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

Here is the DAG of the computational workflow:

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

1. Process PacBio CCSs. Creates a barcode-variant lookup table.

2. Count variants by barcode. Creates a variant counts file giving counts of each barcoded variant in each condition.

3. Fit CGG-binding titration curves to calculate per-barcode K_D, recorded in this file.

4. Fit TuGG-binding titration curves to calculate per-barcode K_D, recorded in this file.

5. Fit polyspecificity reagent binding Sort-seq to calculate per-barcode polyspecificity score, recorded in this file.

6. Analyze Sort-seq to calculate per-barcode RBD expression, recorded in this file.

7. Derive final genotype-level phenotypes from replicate barcoded sequences. Generates final phenotypes, recorded in this file.

   8. Map DMS phenotypes to the CGG-bound antibody structure.