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

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

HydrAMP: a deep generative model for antimicrobial peptide discovery

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

Harmonization of AMR predictor tool outputs

AMR/VF LGT focused bacterial genomics analysis workflow

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

Bacterial Assembly and Antimicrobial Resistance Genes In NextFlow

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.

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

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

Chromosomal mutations associated with nitrofurantoin resistance in Escherichia coli

Pipelines creating allelic presence-absence matrices from SRST2 and ARIBA results

A Jupyter notebook to demonstrate usage of piezo, gumpy and gnomonicus with different AMR catalogues

👨‍💻🧬🤖 deep neural networks: 1Dconvolution experiments with kernel size and stride length

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

Scripts for ARIBA-based gene detection