Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

Making whole bacterial genome sequencing data analysis easy

HydrAMP: a deep generative model for antimicrobial peptide discovery

Code for the paper "Antimicrobial resistance prediction in clinical isolates through machine learning on MALDI-TOF mass spectra"

AMR/VF LGT focused bacterial genomics analysis workflow

An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences

Harmonization of AMR predictor tool outputs

StaphScope is a comprehensive bioinformatics tool for Staphylococcus aureus genomic analysis including MLST typing, spa typing, SCCmec analysis, antimicrobial resistance detection, virulence factors, plasmid profiling, and lineage prediction from whole genome sequencing data. Designed specifically for MRSA research

A data specification for harmonizing One Health AMR pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a spreadsheet collection template, supported by field and reference guides as well as different curation and new term request SOPs.

PhyloTrace is a GUI platform for bacterial monitoring offering a toolkit of analyses like hashed cgMLST typing and Antimicrobial Resistance Screening.

Bacterial Assembly and Antimicrobial Resistance Genes In NextFlow

PRAWNS: A fast and scalable bioinformatics tool that generates an efficient pan-genome representation of closely related whole genomes to provide a concise list of genomic features

Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variants

Implementation of the pipeline described in the work "Artificial intelligence model to predict resistances in Gram-negative bloodstream infections" by Bonazzetti et al., npj Digit. Med. 8, 319 (2025)

Antimicrobial Resistance Test Interpretation Engine

WGS-EPIPE: A Snakemake-driven WGS workflow using Shovill, database comparisons, and Snippy for isolate analysis.

Data and code repository for study aiming to understand ESBL carriage in Blantyre, Malawi

MTB++ a software developed to predict antimicrobial resistance to 13 antibiotics and 3 families of antimicrobials.

Source code for analysis of the impact of environmental and patient-level factors on hospital-acquisition of pathogens