Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

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

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"

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

AMR/VF LGT focused bacterial genomics analysis workflow

Harmonization of AMR predictor tool outputs

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)

# Staphscope Typing Tool A unified MLST + spa + SCCmec typing tool for *Staphylococcus aureus*. ## Features - Multi-locus sequence typing (MLST) - spa typing - SCCmec typing using CGE SCCmecFinder - Parallel processing for high-throughput analysis - Comprehensive reporting in multiple formats

Antimicrobial Resistance Test Interpretation Engine

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

An interactive and user-friendly web application to explore the hospital microbiome and genetic makeup

Here is my participation to the 2024 edition of the HackBio Internship (AMR in cancer track).

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