🔎 💊 Mass screening of contigs for antimicrobial and virulence genes

(Meta-)genome screening for functional and natural product gene sequences

A workflow for analysis and resistance profiling of Mycobacterium tuberculosis nanopore data with Mykrobe

Rapid, in silico characterization of Bacillus cereus group isolates using WGS data

Pure Python port and interface to ABRicate, a tool for mass screening of contigs for antimicrobial resistance or virulence genes.

A companion application for analyzing and viewing BTyper output files in aggregate

Plasmidome analysis to track the transfer route of AMR genes in bacteria

AMU and antimicrobial resistance genes in chicken farms

antimicrobial machine learning

This pipeline takes the raw metagenomic WGS reads as an input, assemble them, separate the contigs in MAGs, taxonomically classify the MAGs and quantify the ARGs in the MAGs. The pipeline is built using R Shiny and people can run end to end analysis by doing few clicks on the screen.

Different approaches to identify best practices for detection of AMR genes, including: total genomic DNA and plasmid DNA extractions, solo assembly of Illumina short-reads and of ONT long-reads, and two hybrid assembly pipelines

Master course thesis project done in 2024 about searching AMR genes in urban wastewater from two cities in Italy: Torino and Novara