This repository contains the workflow and config files for the Dr. PRG paper. See https://github.com/mbhall88/drprg for the Dr. PRG software repository.
To run the pipeline you will need conda and
singularity installed. You can find a
conda environment specification file at environment.yaml.
The CSV files containing the accessions and their associated phenotypes
are config/illumina.samplesheet.csv
and config/nanopore.samplesheet.csv. The
versions of these files with the .pass.csv extension contain only those files that
passed the quality control step we outline in the paper.
The config/samplesheets/ directory contains the individual samplesheets that were used
to construct these main samplesheets.
See workflow/notebook/notepad.ipynb for a
notebook that was used to clean and combine all of these data sources, along with the
links to the publications that generated them.
The version of the repository used for the paper is archived at https://doi.org/10.5281/zenodo.7819984. Within that archive, but not in this GitHub repository, is the population VCF we used to build the M. tuberculosis reference graph.
The 48 common mutations we manually added to this VCF are listed
in resources/target.mutations.tsv.