gta2024-bacterial-genomics.md

---

layout: event-track
redirect_from:
- /events/tracks/gta2024-bacterial-genomeics

title: Bacterial genomics and AMR detection
description: This track explains the basic steps to (1) process, assemble, annotate a bacterial genome and (2) detect Antimicrobial resistance (AMR) genes in bacterial genomes using Galaxy. Start with the tutorial at your own pace. If you need support contact us via the Slack Channel [#gta_bacterial_genomics](https://gtnsmrgsbord.slack.com/archives/C07NE0FHM6H).

slack_channel: gta_bacterial_genomics

contributions:
    organisers:
        - bebatut
        - clsiguret
    instructors:
        - annasyme
        - bebatut
        - clsiguret
        - EngyNasr
        - GarethPrice-Aus
        - igormakunin
        - meltemktn
        - paulzierep
        - SaimMomin12



program:
  - section: "Bacterial genomics" 
    description: |
      Preparation, assembly and annotation of a bacterial genome. If you encounter any issue please ask us in this Slack channel. 
    tutorials:
      - name: quality-contamination-control
        topic: sequence-analysis
      - name: mrsa-illumina
        topic: assembly
      - name: bacterial-genome-annotation
        topic: genome-annotation
  - section: "AMR detection" 
    description: |
      Detect Antimicrobial resistance (AMR) genes in an assembled bacterial genome. If you encounter any issue please ask us in this Slack channel. 
    tutorials:
      - name: amr-gene-detection
        topic: genome-annotation
  - section: "Pathogen detection" 
    description: |
      Pathogen detection. If you encounter any issue please ask us in this Slack channel. 
    tutorials: 
      - name: pathogen-detection-from-nanopore-foodborne-data
        topic: microbiome

---