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.

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

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

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

Antimicrobial Resistance Test Interpretation Engine

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

Chromosomal mutations associated with nitrofurantoin resistance in Escherichia coli

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

Bioinformatics analysis used to determine reinfection and relapse tuberculosis using whole genome sequencing data.