Detection of AMR genes in bacterial genomes
purlPURL: https://gxy.io/GTN:P00018Comment: What is a Learning Pathway?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
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
Lesson | Slides | Hands-on | Recordings |
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Quality and contamination control in bacterial isolate using Illumina MiSeq Data |
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
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 |
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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 |
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Identification of AMR genes in an assembled bacterial genome |
Recommended follow-up tutorials
Lesson | Slides | Hands-on | Recordings |
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Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition |
Editorial Board
This material is reviewed by our Editorial Board:
Bérénice Batut Clea SiguretFunding
These individuals or organisations provided funding support for the development of this resource