data

Input data

PacBio full-length variant sequencing

PacBio_amplicon.gb: Genbank file having features to parse with alignparse. Must have gene (the gene of interest) and barcode features.

PacBio_feature_parse_specs.yaml: How to parse the PacBio amplicon using alignparse.

PacBio_runs.csv: List of PacBio CCS FASTQs used to link barcodes to variants. It must have the following columns:

• library: name of the library sequenced
  • LibA: concatenated A1-48, A2-1, and A2-2 because these represented three sorts of the same pool of cells
  • LibB: concatenated B1-48, B2-1, and B2-2 because these represented three sorts of the same pool of cells
• run: date of the pacbio library submission (use this date to refer to experimental notebook)
  • A1-48: 210423
  • A2-1: 210430
  • A2-2: 210430
  • B1-48: 210423
  • B2-1: 210430
  • B2-2: 210430
  • LibA: concatenated on 220404
  • LibB: concatenated on 220404
• fastq: FASTQ file from running CCS
  • Original PacBio sequencing from the dates listed above is stored in bams so the data was converted to fastq outside of the pipeline and stored in the data folder

Site numbering

site_numbering_map.csv: Maps sequential 1, 2, ... numbering of the gene to a "reference" numbering scheme that represents the standard naming of sites for this gene. Also assigns each site to a region (domain) of the protein. So must have columns sequential_site, reference_site, and region.

Mutation-type classification

data/mutation_design_classification.csv classifies mutations into the different categories of designed mutations. Should have columns sequential_site, amino_acid, and mutation_type.

Neutralization standard barcodes

neutralization_standard_barcodes.csv barcodes for the neutralization standards. Must have columns barcode and name, giving the barcode and name of this neutralization standard set.

Barcode runs

barcode_runs.csv must contain the following columns (you can optionally include more):

• sample: sample name, must be unique among barcode runs. Sample name must begin with <library>-<YYMMDD> where <library> is the library and <YYMMDD> is the date. It is recommended (but not enforced) that the full format be <library>-<YYMMDD>-<description>-<replicate> where <description> is a string description with underscores but no dashes, and <replicate> is a number.
• library: name of library, must match a library in the barcode-variant table
• date: date of sequencing, specified in a format parseable to a date by pandas.
• fastq_R1: path to one more FASTQ R1 sequencing files, multiple files should be semicolon-delimited

Configuration for analyzing functional effects of mutations

func_effects_config.yml has the configuration for analyzing functional effects of mutations. The format is explained within the file.

Configuration for analyzing antibody escape

antibody_escape_config.yml has the configuration for analyzing effects of mutations on escape from antibodies or sera. The format is explained within the file.