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README.md

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Input data

This directory contains input data for the analysis.

Basic information about sequences and alignments

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

  • PacBio_amplicon.gb: the amplicons being sequenced by PacBio.

  • 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.

  • CGGnaive_sites.csv provides a lookup table for converting from scFv CDS indexed site numbeirng to heavy/light chain IMGT numbering