PseudoScope
PseudoScope is an automated, locally-executable computational pipeline designed specifically for comprehensive Pseudomonas aeruginosa genomic surveillance. It integrates seven essential analysis modules into a single, cohesive workflow: FASTA QC (assembly quality metrics), MLST (Oxford scheme), PAST serotyping (O-antigen typing), AMRFinderPlus (antimicrobial resistance gene detection), ABRicate (multi-database screening for resistance, virulence, plasmids, biocides), Ultimate Reporter (gene-centric integration with interactive HTML), and Visualisation Dashboard (publication-ready interactive plots including PCA, networks, boxplots). PseudoScope runs entirely locally (or on HPC clusters), protects data privacy, and produces beautiful interactive reports in minutes.
Topics
Details
- License:
- MIT
- Maturity:
- Mature
- Cost:
- Free of charge
- Tool Type:
- command-line tool, workflow
- Operating Systems:
- Linux, Mac, Windows
- Programming Languages:
- Python
- Added:
- 8/2/2026
- Last Updated:
- 8/2/2026
Operations
Documentation
Command-line options
https://github.com/bbeckley-hub/pseudoscopePseudoScope's documentation, including installation, usage examples, and module descriptions, can be found in the repository's README.
Downloads
- Software packageVersion: v1.2.0https://github.com/bbeckley-hub/pseudoscopePseudoScope can be downloaded and installed via Conda (conda create -n pseudoscope -c conda-forge -c bioconda pseudoscope -y) or used via Docker (docker pull bbeckleyhub/pseudoscope:latest) or Singularity.
Links
Repository
https://github.com/bbeckley-hub/pseudoscope(The link points to PseudoScope's repository. PseudoScope is a species-specific bioinformatics suite for rapid and accessible Pseudomonas aeruginosa genomic surveillance, integrating MLST, serotyping, AMR, virulence detection, and visualisation.)