Name		Name	Last commit message	Last commit date
parent directory ..
barcode_runs_helper_files		barcode_runs_helper_files
pdbs		pdbs
plasmid_maps		plasmid_maps
210801_mutation_counts.csv		210801_mutation_counts.csv
PacBio_amplicons.gb		PacBio_amplicons.gb
PacBio_runs.csv		PacBio_runs.csv
RBD_sites.csv		RBD_sites.csv
README.md		README.md
barcode_runs.csv		barcode_runs.csv
dms-view_metadata.md		dms-view_metadata.md
early2020_escape_profiles_config.yaml		early2020_escape_profiles_config.yaml
escape_profiles_config.yaml		escape_profiles_config.yaml
feature_parse_specs.yaml		feature_parse_specs.yaml
final_variant_scores.csv		final_variant_scores.csv
lineplots_config.yaml		lineplots_config.yaml
output_pdbs_config.yaml		output_pdbs_config.yaml
prelim_variant_dms_scores.csv		prelim_variant_dms_scores.csv
site_color_schemes.csv		site_color_schemes.csv
wildtype_sequence.fasta		wildtype_sequence.fasta
wuhan1_wildtype_sequence.fasta		wuhan1_wildtype_sequence.fasta

README.md

Input data

This directory contains input data for the analysis.

These files are used for the basic processing of the deep sequencing data to call variants by barcode and count barcodes:

PacBio_amplicons.gb: the amplicons being sequenced by PacBio. Note that there are a variety of possible amplicons because in addition to the SARS-CoV-2 RBD there are RBDs from a variety of other viral strains.
feature_parse_specs.yaml: how to parse the amplicon when handling the PacBio data.
PacBio_runs.csv: list of the PacBio runs used to call the variants.
barcode_runs.csv: list of the Illumina runs used to count the barcodes for different samples. This file is built from barcode_runs_orig-names.csv by the Jupyter notebook build_barcode_runs.ipynb.
RBD_sites.csv: gives site and residue information for SARS-CoV-2, including alignment of the RBD integer numbering with the Spike numbering for SARS-CoV-2 RBD, alignment to SARS-CoV, and structural annotations as detailed below.
plasmid_maps: This subdirectory contains the full Genbank maps for key plasmids used in the study: - the wildtype D614G and B.1.351 spike expression plasmids used to make pseudotyped lentiviral particles, - the B.1.351 wildtype RBD yeast-display plasmid, and - the fully assembled plasmid, including the Illumina adaptors and Nx16 barcode, that was used as the template for designing the Twist site-saturation variant libraries.

These files are used for visualizing the antibody- or serum-escape data:

site_color_schemes.csv: Schemes for how to color sites (can be used in escape profiles). Here are details on these schemes.
- The subdomain scheme colors sites orange if they directly contact ACE2 (within 4 angstroms in PDB 6m0j) in the SARS-CoV-2 structure (residues 417, 446, 449, 453, 455, 456, 475, 486, 487, 489, 493, 496, 498, 500, 501, 502, 505), blue if they are in the receptor binding motif (RBM, residue 437 to 508, inclusive), and green if they are in the core RBD domain (all other sites). These definitions match those used in Starr et al (2020).
escape_profiles_config.yaml: Information on how to plot the escape profiles; manually edit this to alter their plotting.