Merge pull request #5261 from bebatut/gta-bacterial-genomics-update

Galaxy Training Academy: Update bacterial genomics track

Author: bgruening

events/galaxy-academy-2024.md

@@ -71,6 +71,8 @@ contributions:
         - by-covid
         - elixir-europe
         - mwk
+        - abromics
+        - ifb
 
 
 location:
@@ -136,7 +138,7 @@ program:
       - title: Microbiome
         link: events/tracks/gta2024-micorbiome.md
       - title: Bacterial Genomics
-        link: events/tracks/gta2024-bacterial-genomeics.md
+        link: events/tracks/gta2024-bacterial-genomics.md
       - title: BY-COVID
         link: events/tracks/gta2024-bycovid.md
       - title: Machine Learning

events/tracks/gta2024-bacterial-genomeics.md

@@ -0,0 +1,44 @@
+---
+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.
+
+contributions:
+    organisers:
+        - bebatut
+        - clsiguret
+    instructors:
+        - bebatut
+        - clsiguret
+        - SaimMomin12
+        - EngyNasr
+
+
+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
+
+---