antimicrobial-resistance

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"

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

UPHL's Reference Free Pipeline

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

Multi-agent research platform for reproducible antimicrobial-resistance genomics exploration, evidence synthesis, and reporting.

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

Antimicrobial Resistance Test Interpretation Engine

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)

Snakemake workflow for bacterial whole-genome sequencing: assembly, QC, taxonomy, annotation, AMR and virulence, plasmids and prophages — plus an optional mobilome module that reports whether each AMR gene sits in a mobile element and how transferable it is. Four entry points: Illumina, Nanopore, hybrid or assembled contigs.

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