From 33d57699aff5e552ed8429220c7ad9f49aefd0fb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= <berenice.batut@gmail.com>
Date: Mon, 13 Jan 2025 13:16:50 +0100
Subject: [PATCH] Modify metagenomics LP: re-order, new tutorials, etc

---
 learning-pathways/metagenomics.md | 50 ++++++++++++++++---------------
 1 file changed, 26 insertions(+), 24 deletions(-)

diff --git a/learning-pathways/metagenomics.md b/learning-pathways/metagenomics.md
index ea5b062484747..66d07d84ff472 100644
--- 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
 ---