Path: blob/main/learning-pathways/amr-gene-detection.md
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---layout: learning-pathway title: Detection of AMR genes in bacterial genomes description: | This learning path aims to teach you the basic steps to detect and check Antimicrobial resistance (AMR) genes in bacterial genomes using Galaxy. type: use tags: [amr, bacteria, microgalaxy, one-health, microbiome] editorial_board: - bebatut - clsiguret funding: - abromics pathway: # - section: "Module 1: Introduction" # description: | # General introduction to AMR detection # #tutorials: # # - name: introduction # # topic: genome-annotation - section: "Module: Species and contamination checking" description: | Quality control and taxonomic assignation is useful in AMR detection to verify the quality of the data but also to check contamination and confirm species tutorials: - name: quality-contamination-control topic: sequence-analysis - section: "Module: Assembly" description: | 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 tutorials: - name: mrsa-illumina topic: assembly - name: mrsa-nanopore topic: assembly - section: "Module: Genome annotation" description: | 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 tutorials: - name: bacterial-genome-annotation topic: genome-annotation - section: "Module: AMR gene detection" description: | AMR gene content can be assessed from the contigs to detect known resistance mechanisms and potentially identify novel mechanisms. tutorials: - name: amr-gene-detection topic: genome-annotation - section: "Recommended follow-up tutorials" tutorials: - name: pathogen-detection-from-nanopore-foodborne-data topic: microbiome
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