Code for analysis of Borrelia burgdorferi genomes
Jacob E. Lemieux Broad Institute
A preprint is here: https://www.biorxiv.org/content/10.1101/2023.02.26.530159v1
notebooks/Bbss_main_figures_revision.R for the notebook that implements the analysis and generates most of the figures notebooks/Run_pan_genome_associations.py generates the Manhattan plots
assemblies are in data/ fastq files are in SRA under PRJNA923804 (release date of June 8 2023)
pipeline to generate the assemblies: scripts/preprocess_assemblies.sh