Detection of AMR genes in bacterial genomes

Comment: What is a Learning Pathway?
A graphic depicting a winding path from a start symbol to a trophy, with tutorials along the way
We recommend you follow the tutorials in the order presented on this page. They have been selected to fit together and build up your knowledge step by step. If a lesson has both slides and a tutorial, we recommend you start with the slides, then proceed with the tutorial.

This learning path aims to teach you the basic steps to detect and check Antimicrobial resistance (AMR) genes in bacterial genomes using Galaxy.

Module: Species and contamination checking

Taxonomic assignation is useful in AMR detection to check contamination and confirm species

Lesson Slides Hands-on Recordings
Checking expected species and contamination in bacterial isolate

Module: Assembly

Assembly is a major step in the process of detecting AMR genes as it combines sequenced reads into contigs, longer sequences where it will be easier to identify genes and in particular AMR genes

Lesson Slides Hands-on Recordings
Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data
Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)

Module: Genome annotation

The generated contigs can be annotated to detect genes, potential plasmids, etc. This will help the AMR gene detection process, especially the verification and visualization

Lesson Slides Hands-on Recordings
Bacterial Genome Annotation

Module: AMR gene detection

AMR gene content can be assessed from the contigs to detect known resistance mechanisms and potentially identify novel mechanisms.

Lesson Slides Hands-on Recordings
Identification of AMR genes in an assembled bacterial genome

Lesson Slides Hands-on Recordings
Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition

Editorial Board

This material is reviewed by our Editorial Board:

orcid logoBérénice Batut avatar Bérénice Batut


This material was funded by:

ABRomics avatar ABRomics