bbeckleyhub/pseudoscope

By bbeckleyhub

•Updated about 2 months ago

🧬 PseudoScope – Docker Image

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Data science

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bbeckleyhub/pseudoscope repository overview

⁠🧬 PseudoScope – Docker Image

Complete MLST, serotyping, AMR, virulence & visualisation for Pseudomonas aeruginosa – in minutes

⁠🚀 Quick Start

# Pull the image
docker pull bbeckleyhub/pseudoscope:latest

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

Note: The image includes pre‑installed ABRicate and AMRfinderPlus databases – no extra setup needed. Just pull and run!

⁠📋 Table of Contents

Quick Start⁠
Usage Examples⁠
Command‑line Options⁠
Output Structure⁠ ← Updated with actual layout
Core Modules⁠
Singularity (HPC)⁠
Citation⁠
Support⁠

⁠📖 Usage Examples

⁠Basic single genome analysis

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

⁠Batch processing with glob pattern

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

⁠Skip specific modules (faster test run)

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

⁠Keep temporary files for debugging

docker run --rm \
  -v $(pwd):/data \
  -w /data \
  bbeckleyhub/pseudoscope:latest \
  -i "*.fna" -o debug_run --keep-temp

⁠Update AMR database (if needed)

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

⁠⚙️ Command‑line Options

Flag	Description
`-i`, `--input`	Input FASTA file(s) – supports glob patterns (e.g., `"*.fna"`)
`-o`, `--output`	Output directory for all results
`-t`, `--threads`	Number of CPU threads (default: 2)
`--quiet`	Suppress all non‑error output
`--version`	Show version and exit
`--update-amr-db`	Update AMRfinderPlus database and exit
`--skip-qc`	Skip FASTA QC
`--skip-mlst`	Skip MLST
`--skip-past`	Skip PAST serotyping
`--skip-abricate`	Skip ABRicate
`--skip-amr`	Skip AMRfinderPlus
`--skip-summary`	Skip ultimate reporter
`--skip-viz`	Skip visualisation dashboard
`--keep-temp`	Keep temporary directories (debugging)

Supported FASTA formats: .fna, .fasta, .fa, .fn

⁠📁 Output Structure

Below is the actual output tree generated by PseudoScope (from a real run). All paths are relative to your specified output directory (-o).

results/
├── fasta_qc_results/                          # QC per sample + summary
│   ├── {sample}/
│   │   ├── {sample}_fasta_qc_report.html
│   │   └── {sample}_fasta_qc_report.json
│   ├── PseudoScope_FASTA_QC_summary.html
│   ├── PseudoScope_FASTA_QC_summary.json
│   └── PseudoScope_FASTA_QC_summary.tsv
│
├── mlst_results/                              # MLST per sample + summary
│   ├── {sample}/
│   │   ├── mlst_raw_output.txt
│   │   ├── mlst_report.html
│   │   ├── mlst_report.json
│   │   ├── mlst_report.tsv
│   │   └── mlst_report.txt
│   ├── mlst_summary.csv
│   ├── mlst_summary.html
│   └── mlst_summary.json
│
├── past_results/                              # PAST serotyping per sample + summary
│   ├── {sample}/
│   │   ├── {sample}.blastn.tsv
│   │   ├── {sample}.details.tsv
│   │   ├── {sample}.tsv
│   │   ├── past_report.html
│   │   ├── past_report.json
│   │   ├── past_report.tsv
│   │   ├── past_report.txt
│   │   └── pasty_run.log
│   ├── past_summary.csv
│   ├── past_summary.html
│   └── past_summary.json
│
├── pseudo_abricate_results/                   # ABRicate per sample & per database summaries
│   ├── {sample}/
│   │   ├── abricate_{db}_report.html   (for each database: argannot, bacmet2, card, ecoh, ecoli_vf, megares, ncbi, plasmidfinder, resfinder, vfdb)
│   │   ├── abricate_{db}.txt
│   │   └── {sample}_comprehensive_abricate_report.html
│   ├── pseudo_abricate_master_summary.json
│   ├── pseudo_{db}_summary_report.html
│   ├── pseudo_{db}_summary.json
│   └── pseudo_{db}_abricate_summary.tsv
│
├── pseudo_amrfinder_results/                  # AMRfinder per sample + mutation summary
│   ├── {sample}/
│   │   ├── {sample}_amrfinder_report.html
│   │   ├── {sample}_amrfinder_report.json
│   │   ├── {sample}_amrfinder_summary.json
│   │   ├── {sample}_amrfinder.txt
│   │   ├── {sample}_mutations.html
│   │   └── {sample}_mutations.tsv
│   ├── pseudo_amrfinder_master_summary.json
│   ├── pseudo_amrfinder_statistics_summary.tsv
│   ├── pseudo_amrfinder_summary_report.html
│   ├── pseudo_amrfinder_summary.tsv
│   ├── mutation_master_summary.json
│   ├── mutation_summary.html
│   └── mutation_summary.tsv
│
├── GENIUS_PSEUDOMONAS_ULTIMATE_GENE_CENTRIC_REPORTS/   # Gene‑centric integrated report (all samples)
│   ├── genius_pseudomonas_ultimate_gene_centric_report.html  ← **Main gene‑centric report**
│   ├── genius_pseudomonas_ultimate_gene_centric_report.json
│   ├── amr_genes.csv
│   ├── virulence_genes.csv
│   ├── bacmet_genes.csv
│   ├── mutations.csv
│   ├── sample_overview.csv
│   └── gene_cooccurrence.csv
│
├── GENIUS_PSEUDOMONAS_SAMPLE_CENTRIC_REPORTS/           # Sample‑centric (isolate‑based) report
│   ├── genius_pseudomonas_sample_centric_report.html    ← **Main sample‑centric report**
│   ├── genius_pseudomonas_sample_centric_report.json
│   ├── amr_genes.csv
│   ├── virulence_genes.csv
│   ├── bacmet_genes.csv
│   ├── sample_overview.csv
│   └── gene_cooccurrence.csv
│
├── GENIUS_PSEUDOMONAS_VISUAL_DASHBOARD/                # Interactive visualisation dashboard
│   └── genius_pseudomonas_visual_dashboard.html        ← **Interactive plots (Plotly)**
│
└── pseudoscope_run.log                                 # Full run log (debugging & reproducibility)

⁠📌 Key files to open

File	Purpose
`GENIUS_PSEUDOMONAS_ULTIMATE_GENE_CENTRIC_REPORTS/genius_pseudomonas_ultimate_gene_centric_report.html`	Gene‑centric – each gene shows all samples carrying it; sortable, searchable, filterable.
`GENIUS_PSEUDOMONAS_SAMPLE_CENTRIC_REPORTS/genius_pseudomonas_sample_centric_report.html`	Sample‑centric – each sample has a dedicated box with all its AMR, virulence, and bacmet genes.
`GENIUS_PSEUDOMONAS_VISUAL_DASHBOARD/genius_pseudomonas_visual_dashboard.html`	Interactive plots – PCA, co‑occurrence network, bar charts, boxplots, heatmaps.

⁠🔍 Core Modules

Module	Purpose	Outputs
FASTA QC	Assembly quality metrics	N50, GC%, contig stats, HTML/TSV/JSON
MLST	Oxford scheme ST assignment	ST, 7‑gene profile, summary table
PAST	O‑serotyping	O‑type (O1–O20), coverage, hits
AMRfinderPlus	AMR gene detection	Risk categories, per‑gene prevalence, mutations
ABRicate	Multi‑database screening	Resistance, virulence, plasmids, biocides (10 databases)
Ultimate Gene‑Centric Reporter	Gene‑centric integration	Interactive HTML, CSV exports, per‑gene prevalence
Sample‑Centric Reporter	Isolate‑centric view	Per‑sample gene boxes, summary tables
Visualisation Dashboard	Interactive plots	PCA, networks, boxplots, heatmaps

⁠🐳 Singularity (HPC)

For HPC clusters where Docker is not available:

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

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

All output files will be owned by your HPC user – no sudo chown needed.

⁠📚 Citation

If you use PseudoScope in your research, please cite:

@software{beckley2026pseudoscope,
  author = {Brown Beckley},
  title = {PseudoScope: A species‑specific bioinformatics suite for rapid and accessible Pseudomonas aeruginosa genomic analysis},
  year = {2026},
  publisher = {GitHub},
  url = {https://github.com/bbeckley-hub/pseudoscope},
  version = {1.2.0}
}

Integrated tools: Please also cite MLST, ABRicate, PAST, AMRFinderPlus, PubMLST, CARD, ResFinder, VFDB, and others (full list in the repository).

⁠🤝 Support & Contributions

Issues & feature requests: GitHub Issues⁠
Email: [email protected]⁠
Documentation: bbeckley-hub.github.io/pseudoscope⁠

⁠📄 License

The PseudoScope pipeline code is licensed under the MIT License. Third‑party tools are used under their respective licenses.

⭐ If you find PseudoScope useful, please star the repository! ⭐

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docker pull bbeckleyhub/pseudoscope