AcinetoScope
AcinetoScope is an automated, comprehensive bioinformatics pipeline designed specifically for the genomic analysis of Acinetobacter baumannii, a WHO Critical Priority pathogen responsible for devastating hospital-acquired infections. It integrates seven analysis types (MLST, ABRicate, AMRFinder, Kaptive 3, APT, PlasmidFinder, and mutation detection) into a single automated workflow — from FASTA to actionable insights. The pipeline offers both gene-centric and sample-centric reporting, dynamic grouping by typing, and is optimised for HPC, cloud, and container environments.
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/acinetoscopeAcinetoScope's documentation, including installation, usage examples, and module descriptions, can be found in the repository's README.
Downloads
- Software packageVersion: v1.3.1https://github.com/bbeckley-hub/acinetoscopeAcinetoScope can be downloaded and installed via Conda (conda create -n acinetoscope -c conda-forge -c bioconda acinetoscope -y) or used via Docker (docker pull bbeckleyhub/acinetoscope:latest) or Singularity.
Links
Repository
https://github.com/bbeckley-hub/acinetoscope(The link points to AcinetoScope's repository. AcinetoScope is a species-specific computational pipeline for rapid, comprehensive Acinetobacter baumannii outbreak investigation and resistance gene tracking.)