bbeckleyhub/staphscope repository overview

# Pull the image
docker pull bbeckleyhub/staphscope:2.0.0

# Single genome (correct file ownership – no padlock)
docker run --rm \
  -u $(id -u):$(id -g) \
  -v "$(pwd):/data" \
  bbeckleyhub/staphscope:2.0.0 \
  -i "/data/my_genome.fna" -o /data/results

# Batch processing
docker run --rm \
  -u $(id -u):$(id -g) \
  -v "$(pwd):/data" \
  bbeckleyhub/staphscope:2.0.0 \
  -i "/data/*.fna" -o /data/results --threads 8

docker run --rm \
  -u $(id -u):$(id -g) \
  -v "$(pwd):/data" \
  bbeckleyhub/staphscope:2.0.0 \
  -i "/data/SA001.fasta" -o /data/SA001_results

docker run --rm \
  -u $(id -u):$(id -g) \
  -v "$(pwd):/data" \
  bbeckleyhub/staphscope:2.0.0 \
  -i "/data/*.fna" -o /data/batch_results --threads 16

docker run --rm \
  -u $(id -u):$(id -g) \
  -v "$(pwd):/data" \
  bbeckleyhub/staphscope:2.0.0 \
  -i "/data/*.fasta" -o /data/results \
  --skip-mge --skip-amr --skip-abricate --skip-visualization

docker run --rm \
  -u $(id -u):$(id -g) \
  -v "$(pwd):/data" \
  bbeckleyhub/staphscope:2.0.0 \
  -i "/data/*.fna" -o /data/results \
  --skip-mge --skip-capsule --skip-sccmec-rpet

docker run --rm \
  -u $(id -u):$(id -g) \
  -v "$(pwd):/data" \
  bbeckleyhub/staphscope:2.0.0 \
  -i "/data/*.fna" -o /data/results \
  --amr-min-identity 0.95 --amr-min-coverage 0.9 --skip-amr-mutations

docker run --rm \
  -u $(id -u):$(id -g) \
  -v "$(pwd):/data" \
  bbeckleyhub/staphscope:2.0.0 \
  -i "/data/*.fna" -o /data/results --clean-output

docker run --rm -it \
  -u $(id -u):$(id -g) \
  -v "$(pwd):/data" \
  bbeckleyhub/staphscope:2.0.0 bash

# 1. Load runtime + mksquashfs (needed only for pull)
module load containers/singularity/3.6.4   # or: module load apptainer
module load squashfs-tools/4.4             # only for the pull

# 2. Pull the image (one-time, needs internet on login node)
singularity pull staphscope_2.0.0.sif docker://bbeckleyhub/staphscope:2.0.0

# 3. Run — always use `run`, not `exec`
singularity run --bind $(pwd):/data \
  staphscope_2.0.0.sif \
  -i "/data/*.fna" -o /data/output -t 16

#!/bin/bash
#SBATCH --job-name=staphscope
#SBATCH --cpus-per-task=16
#SBATCH --mem=32G
#SBATCH --time=04:00:00

module load containers/singularity/3.6.4
cd $SLURM_SUBMIT_DIR

singularity run --bind $(pwd):/data \
  /path/to/staphscope_2.0.0.sif \
  -i "/data/*.fna" -o /data/output -t ${SLURM_CPUS_PER_TASK}

results/
├── Staphscope_final_report/                    # 👈 The folder you need
│   ├── staphscope_comprehensive_report.html
│   ├── staphscope_comprehensive_report.json
│   ├── staphscope_comprehensive_report.tsv    # Master typing TSV
│   ├── STAPHSCOPE_ULTIMATE_GENE_CENTRIC_REPORTS/
│   │   ├── staphscope_ultimate_gene_centric_report.html
│   │   ├── amr_genes.csv
│   │   ├── virulence_genes.csv
│   │   ├── bacmet_genes.csv
│   │   ├── plasmid_replicons.csv
│   │   ├── mutations.csv
│   │   ├── mge_profile.csv
│   │   ├── fasta_qc.csv
│   │   └── sample_overview.csv
│   └── STAPHSCOPE_ULTIMATE_SAMPLE_CENTRIC_REPORTS/
│       ├── staphscope_ultimate_sample_centric_report.html
│       └── staphscope_ultimate_sample_centric_report.json
├── STAPHSCOPE_VISUALIZATIONS/                  # Interactive dashboard + static exports
│   ├── staphscope_dashboard.html              # ← Plotly dashboard, single file
│   ├── PNG/  PDF/  SVG/  DATA/
│   └── staphscope_visualizations_bundle.zip
├── mge_results/                                # Per-module outputs
├── mlst_results/
├── spa_results/
├── sccmec_cge_results/
├── sccmec_rpet_results/
├── capsule_results/
├── agr_results/
├── staph_amrfinder_results/
├── abricate_results/
├── fasta_qc_results/
└── staphscope_run.log

mkdir -p test_data
wget -O test_data/SA.fna \
  https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/013/425/GCF_000013425.1_ASM1342v1/GCF_000013425.1_ASM1342v1_genomic.fna

docker run --rm \
  -u $(id -u):$(id -g) \
  -v "$(pwd)/test_data:/data" \
  bbeckleyhub/staphscope:2.0.0 \
  -i "/data/*.fna" -o /data/results --threads 4

firefox test_data/results/STAPHSCOPE_VISUALIZATIONS/staphscope_dashboard.html

git clone https://github.com/bbeckley-hub/staphscope-typing-tool.git
cd staphscope-typing-tool
docker build -t staphscope:custom .

git clone https://github.com/bbeckley-hub/staphscope-toolkit.git
cd staphscope-toolkit
pip install -r requirements.txt

python staphscope_itol.py --input_dir /path/to/Staphscope_final_report

@article{beckley2026staphscope,
  title={StaphScope: a species-optimized computational pipeline for rapid and accessible Staphylococcus aureus genotyping and surveillance},
  author={Beckley, Brown and Amarh, Vincent},
  journal={BMC Genomics},
  volume={27},
  pages={123},
  year={2026},
  doi={10.1186/s12864-026-12609-x}
}