- recipe acinetoscope
AcinetoScope: Comprehensive A. baumannii genomic typing pipeline with parallel execution
- Homepage:
- License:
MIT
- Recipe:
AcinetoScope is a complete, automated genomic analysis pipeline for Acinetobacter baumannii, featuring parallel execution for rapid processing of bacterial genomes. The pipeline integrates multiple analysis modules into a unified workflow:
Quality Control (FASTA QC) - Comprehensive sequence validation
Multi-Locus Sequence Typing (MLST) - Oxford & Pasteur schemes
K/O Locus Typing (Kaptive) - Capsule and lipooligosaccharide typing
Antimicrobial Resistance (AMR) - Comprehensive resistance gene detection
Virulence & Plasmid Profiling (ABRicate) - Multi-database screening
Critical Genes Flagging - Priority markers for infection control
Interactive HTML Reports - Gene-centric integrated analysis
Cross-genome pattern discovery
Key Features: 🚀 Parallel Execution - All modules run simultaneously for maximum speed 📊 Interactive Reports - HTML summaries with visualization 🧬 Multi-Database Integration - CARD, ResFinder, VFDB, NCBI, MEGARes, BacMet ⚡ Easy Deployment - Single command analysis with automatic dependency handling 🎯 Critical Gene Tracking - Carbapenemases, ESBLs, colistin/tigecycline resistance
Designed for clinical microbiology, outbreak investigation, and genomic surveillance, AcinetoScope provides clinical labs and researchers with a complete solution for A. baumannii genomic characterization from raw sequencing data to publication-ready reports.
- package acinetoscope¶
- Versions:
1.1.0-0- Depends:
on abricate
>=1.2.0on any2fasta
on beautifulsoup4
>=4.11.0on biopython
>=1.85on blast
>=2.13.0on click
>=8.0.0on kaptive
>=3.1.0on lxml
>=4.9.0on matplotlib-base
>=3.5.0on pandas
>=1.5.0on perl
on perl-data-dumper
on perl-file-which
on perl-getopt-long
on perl-json
on perl-list-moreutils
on perl-lwp-protocol-https
on perl-moo
on perl-path-tiny
on plotly
>=5.10.0on psutil
>=5.9.0on python
>=3.9on requests
>=2.28.0on scipy
>=1.10.1on seaborn
>=0.12.0on tqdm
>=4.64.1
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install acinetoscope
to add into an existing workspace instead, run:
pixi add acinetoscope
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install acinetoscope
Alternatively, to install into a new environment, run:
conda create -n envname acinetoscope
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/acinetoscope:<tag>
(see acinetoscope/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/acinetoscope/README.html)
