RADS-Bacillota

Release Notes: v1.0.0 — Bacillota Defense System Analysis

Overview

This repository contains the complete results of running the RADS pipeline against 13,553 Bacillota genomes using the EF_B0058 recombinase as the query sequence. It accompanies the RADS publication and provides an interactive dashboard and shareable HTML report for exploring defense systems flanking recombinase genes across the Bacillota phylum.

RADS was developed by Shelby E Andersen in collaboration with Joshua M Kirsch, Jay R Hesselberth, and Breck A Duerkop.

Dataset

| Metric | Value | |---|---| | Phylum | Bacillota (Firmicutes) | | Query | EF_B0058 recombinase | | Total genomes | 13,553 | | BLAST hits | 9,478 | | Hits per Mb | 0.215 | | Contigs analyzed | 8,656 | | Defense genes identified | 4,176 | | Co-transcribed ORFs | 2,827 |

Full results are in results/efb0058_bacillota_withbinom_complete/.

Contents

results/efb0058_bacillota_withbinom_complete/
├── blast_results/master_blast.txt         # BLAST hits (query vs all genomes)
├── defensefinder/
│   ├── defense_finder_genes.tsv           # Per-gene defense annotations
│   └── defense_finder_systems.tsv         # Per-system annotations
├── cotranscription/                        # Co-transcribed ORF analysis
├── interproscan_results.tsv               # Domain annotations (InterPro/Pfam)
├── BinomialAnalysis.csv                   # Enriched domains (binomial test)
├── defense_scores.tsv                     # Defense context scores
├── metrics/pipeline_metrics.json          # Run statistics
├── figures/                               # Publication PDFs
└── defense_plots.py                       # Figure generation script

Publication Figures

Defense system figures are in results/efb0058_bacillota_withbinom_complete/figures/:

| File | Content | |---|---| | 1_AB_categories_heatmap.pdf | A: Category bar chart; B: Family × category heatmap | | 2_top_two_categories.pdf | Top two categories broken down by system type | | 3_defense_scores.pdf | Defense score distribution for co-transcribed ORFs |

To regenerate figures:

# Pixi
pixi run python results/efb0058_bacillota_withbinom_complete/defense_plots.py
 
# Conda
conda activate rads
python results/efb0058_bacillota_withbinom_complete/defense_plots.py

Interactive Dashboard

Pixi (recommended):

git clone https://github.com/Seandersen/RADS-Bacillota.git
cd RADS-Bacillota
curl -fsSL https://pixi.sh/install.sh | bash   # skip if Pixi already installed
pixi install
pixi run dashboard

Conda/Mamba:

git clone https://github.com/Seandersen/RADS-Bacillota.git
cd RADS-Bacillota
conda env create -f environment.yaml
conda activate rads
python -m shiny run dashboard/app.py --host 0.0.0.0 --port 8000

Open http://localhost:8000 in your browser.

HPC / Remote server: Use an SSH tunnel to forward the port to your local machine:

ssh -N -L 8000:<node>:8000 <user>@<server>

Shareable HTML Report

A self-contained HTML report can be generated with no server required:

# Pixi
pixi run python workflow/scripts/generate_report.py \
    --results results/efb0058_bacillota_withbinom_complete \
    --output  results/efb0058_bacillota_withbinom_complete/report.html
 
# Conda
conda activate rads
python workflow/scripts/generate_report.py \
    --results results/efb0058_bacillota_withbinom_complete \
    --output  results/efb0058_bacillota_withbinom_complete/report.html

Add --include-locus-viewer to embed gene-arrow diagrams (produces a larger file).

Reproducibility

This dataset was generated with the RADS pipeline. The environment is fully specified in environment.yaml and pixi.toml. See the pipeline repository for full documentation on running your own analysis.

Citation

Andersen SE, Kirsch JM, Hesselberth JR, Duerkop BA. RADS: Recombinase Associated Defense Search. [Publication details pending]

MIT License. See LICENSE for details.