bbeckleyhub/enteroscope repository overview

# Pull the image
docker pull bbeckleyhub/enteroscope:latest

# Run analysis on all .fasta files in current directory
docker run --rm \
  -v $(pwd):/data \
  -w /data \
  bbeckleyhub/enteroscope:latest \
  -i "*.fna" -o results --threads 4

docker run --rm \
  -v $(pwd):/data \
  -w /data \
  bbeckleyhub/enteroscope:latest \
  -i genome.fna -o results

docker run --rm \
  -v $(pwd):/data \
  -w /data \
  bbeckleyhub/enteroscope:latest \
  -i "*.fna" -o batch_results --threads 16

docker run --rm \
  -v $(pwd):/data \
  -w /data \
  bbeckleyhub/enteroscope:latest \
  -i "*.fna" -o quick_test --skip-abricate --skip-amr

docker run --rm \
  -v $(pwd):/data \
  -w /data \
  bbeckleyhub/enteroscope:latest \
  -i "*.fna" -o custom_results \
  --amr-min-identity 0.95 --amr-min-coverage 0.9 \
  --abricate-min-identity 85 --abricate-min-coverage 85

docker run --rm \
  -v $(pwd):/data \
  -w /data \
  bbeckleyhub/enteroscope:latest \
  -i "*.fna" -o results --amr-force-update

docker run --rm bbeckleyhub/enteroscope:latest --update-amr-db

Enteroscope_results/
├── fasta_qc_results/                          # QC per sample + summary
│   ├── {sample}_fasta_qc_report.html/json
│   └── Enteroscope_FASTA_QC_summary.html/json/tsv
│
├── mlst_results/                              # MLST per sample + summary
│   ├── {sample}/mlst_report.html/json/txt/tsv
│   └── mlst_summary.html/csv/json
│
├── enteroscope_abricate_results/              # ABRicate per sample & per database summaries
│   ├── {sample}/abricate_{db}_report.html/txt (for each db)
│   └── enteroscope_{db}_summary_report.html/json/tsv (per database)
│
├── enteroscope_amrfinder_results/             # AMRfinder per sample + mutation summary
│   ├── {sample}/{sample}_amrfinder_report.html/json/txt
│   ├── {sample}/{sample}_mutations.html/tsv
│   ├── enteroscope_amrfinder_summary_report.html
│   └── mutation_summary.html/tsv (gene‑centric mutation table)
│
├── ENTERO_ULTIMATE_REPORTS/                   # Final interactive dashboard
│   ├── enteroscope_ultimate_report.html       ← Main interactive report
│   ├── enteroscope_ultimate_report.json       # AI‑ready full data
│   ├── amr_genes.csv
│   ├── virulence_genes.csv
│   ├── bacmet_genes.csv
│   ├── plasmid_markers.csv
│   ├── mutations.csv                          # Exported point mutations
│   ├── enterobacter_samples.csv
│   └── mlst_distribution.csv
│
└── enteroscope_run.log                        # Detailed log file

# Pull directly from Docker Hub
singularity pull enteroscope.sif docker://bbeckleyhub/enteroscope:latest

# Run with writable tmpfs (essential for EnteroScope)
singularity run --writable-tmpfs -B $(pwd):/data enteroscope.sif \
  -i "/data/*.fna" -o /data/output --threads 8

@software{beckley2026enteroscope,
  author = {Brown Beckley},
  title = {EnteroScope: A Tailored Computational Workflow Enabling Rapid, User-Friendly Genotyping and Epidemiological Surveillance of the Enterobacter cloacae Complex},
  year = {2026},
  publisher = {GitHub},
  url = {https://github.com/bbeckley-hub/enteroscope},
  version = {1.1.0}
}