Making whole bacterial genome sequencing data analysis easy

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

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

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

Harmonization of AMR predictor tool outputs

AMR/VF LGT focused bacterial genomics analysis workflow

Antimicrobial resistance prediction app for KBase

Detect the presence of specific resistance genes in a sample using the IRIDA system

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

Antimicrobial Resistance Test Interpretation Engine

Scripts for ARIBA-based gene detection

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

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

Proof-of-concept for storing and querying harmonized AMR Genomic Analysis Results in datahike

Chromosomal mutations associated with nitrofurantoin resistance in Escherichia coli

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

In this repository, we have compiled the WGS analysis schematics of the bacterial isolates obtained from poultry manure of layer and broiler poultry farms