Modify metagenomics LP: re-order, new tutorials, etc

galaxyproject · Jan 13, 2025 · 33d5769 · 33d5769
1 parent 4701c12
commit 33d5769
Showing 1 changed file with 26 additions and 24 deletions.
diff --git a/learning-pathways/metagenomics.md b/learning-pathways/metagenomics.md
@@ -41,19 +41,7 @@ pathway:
       - name: quality-control
         topic: sequence-analysis
 
-  - section: "Module 4: Assembly"
-    description: |
-        This module covers the following questions:
-        - Why metagenomic data should be assembled?
-        - What is the difference between co-assembly and individual assembly?
-        - What is the difference between reads, contigs and scaffolds?
-        - How tools based on De Bruijn graph work?
-        - How to assess the quality of metagenomic data assembly?
-    tutorials:
-      - name: metagenomics-assembly
-        topic: microbiome
-
-  - section: "Module 5: Community taxonomic profiling"
+  - section: "Module 4: Community taxonomic profiling"
     description: |
         This module covers the following questions:
         - Which species (or genera, families, ...) are present in my sample?
@@ -64,26 +52,38 @@ pathway:
     tutorials:
       - name: taxonomic-profiling
         topic: microbiome
-        #description: More theoretical tutorial
       - name: beer-data-analysis
         topic: microbiome
-        #description: Application tutorial
 
-  - section: "Module 6: Taxonomic binning"
+  - section: "Module 5: Community diversity"
+    description: |
+       This module covers the following questions:
+        - How many different taxons are present in my sample? How do I additionally take their relative abundance into account?
+        - How similar or how dissimilar are my samples in term of taxonomic diversity?
+        - What are the different metrics used to calculate the taxonomic diversity of my samples?
+    tutorials:
+      - name: diversity
+        topic: microbiome
+
+  - section: "Module 6: Assembly"
+    description: |
+        This module covers the following questions:
+        - Why metagenomic data should be assembled?
+        - What is the difference between co-assembly and individual assembly?
+        - What is the difference between reads, contigs and scaffolds?
+        - How tools based on De Bruijn graph work?
+        - How to assess the quality of metagenomic data assembly?
+    tutorials:
+      - name: metagenomics-assembly
+        topic: microbiome
+
+  - section: "Module 7: Taxonomic binning"
     description:  |
       This module covers the process used to classify DNA sequences obtained from metagenomic sequencing into discrete groups, or bins, based on their similarity to each other.
     tutorials:
       - name: metagenomics-binning
         topic: microbiome
 
-
-  #- section: "Module 7: Community Biodiversity"
-  #  description:
-  #
-  #  tutorials:
-  #    - name: learner_participation_engagement
-  #      topic: microbiome
-
   - section: "Module 8: Applying concepts to metatranscriptomics data"
     description: |
         This module covers the following questions:
@@ -96,6 +96,8 @@ pathway:
 
   - section: "Recommended follow-up tutorials"
     tutorials:
+      - name: metaplasmidome_query
+        topic: microbiome
       - name: pathogen-detection-from-nanopore-foodborne-data
         topic: microbiome
 ---