Long read assemblies reveal Borrelia burgdorferi population variation structured by plasmids, plasmid subtypes, and genetic networks

Preprint: https://doi.org/10.1101/2025.01.29.635312

This repository contains all code and sequences used in the above manuscript.

Ensure you have git lfs installed to access all files and data. (Instructions below)

Total repository size: 27G

Directory Structure

• assemblies/ - all assemblies and annotations used in our analyses are housed here. The subdirectory name is Strain_ID from table_s1.
  • Each assembly has the following contents:
    • *.embl
    • *.faa
    • *.ffn
    • *.fna
    • *.gbff
    • *.gff3
    • *.hypotheticals.faa
    • *.hypotheticals.tsv
    • *.inference.tsv
    • *.json
    • *.log
    • *.tsv
    • *.txt
• containers/ - all containers used in these analyses are defined here. Contains submodule: mjf-containers
• group2BB/ - Code used to map roary pangene groups back to B31 genes.
• metadb/ - Code used to setup and query an sqlite3 database containing all assemblies and their annotations.
• notebooks/ - Jupyter notebooks used throughout development. Some notebooks may be superceded by scripts present in scripts/
• output/ - Contains all output used in the analysis and figure generation.
  • alignments/ - contains alignments for all vs all, all vs B31.
  • genotyping/ - contains OspC and MLST typing results as well as plasmid calls.
  • homology_networks/ - contains homology network graphs and network.json used to render graph in Blender.
  • reports/ - contains AGAT stats, kraken2, quast, and multiqc reports.
  • results/ - contains roary and panaroo pangenome output for split and non-split paralogs.
• ref/ - contains database of assemblies, B31 reference genome, and replicon references used in classification.
• scripts/ - contains scripts and commands used in various analyses.
• VAE/ - All code and data for variable autoencoder analyses
• scaffolding/ - contains data for scaffolding analyses.
• figures/ - contains notebooks, data, scripts, and relevant files to reproduce published figures. Paths in notebooks are relative to repository root.
• interactive/ - interactive RShiny app for Figure 2 and Figure 6. Requires R-Studio.

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In situations where code or data are unable to be located, refer to our working repository or open an issue!

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Using LFS to access files and data

To get started, clone the repository and setup LFS:

git clone https://github.com/broadinstitute/Bb_pangenome.git
cd Bb_pangenome
git lfs install 

To retrieve LFS tracked files individually:

git lfs fetch path/to/lfs-tracked-file.ext
git lfs checkout

To retrieve LFS tracked directories:

git lfs fetch path/to/lfs-tracked-directory/
git lfs checkout

To retrieve all files and data:

git lfs fetch --all
git lfs checkout