Restructure TOC

README.md

@@ -16,6 +16,6 @@ and with the conda environment activated, in the top directory, run:
 jupyter-book build .
 ```
 The html pages can be found inside `_build`, and
-the home page for the book can be found at `_build/index.html`.
+the home page for the book can be found at `_build/html/index.html`.
 
 All software dependencies are encapsulated in the Docker container that can be downloaded from the Github Packages link associated with this repository. See Getting Started for more information.

_toc.yml

@@ -9,5 +9,8 @@ chapters:
 - file: data-sneak-peek.ipynb
 - file: data-analysis-overview
 - file: taxonomic-profiling
+  sections: 
+  - file: metaphlan.ipynb
+  - file: kraken2.ipynb
 - file: antibiotic-resistance
-- file: going-beyond
+- file: going-beyond

getting-started.md

@@ -10,15 +10,15 @@ To get started, you will need to go through the following steps.
 
 
 ## 1. Download Jupyter notebooks
-Jupyter notebooks needed for this workshop are provided in the GitHub repository: [https://github.com/bioinfodlsu/metagenomics-workshop]. Click the (green) Code button, then download zip, then unzip, and place the `metagenomics-workshop-main` folder to your preferred location. 
+Jupyter notebooks needed for this workshop are provided in the GitHub repository: https://github.com/bioinfodlsu/metagenomics-workshop. Click the (green) Code button, then download zip, then unzip, and place the `metagenomics-workshop-main` folder to your preferred location. 
 
 ## 2. Download dataset 
 A dataset containing pre-downloaded databases and some metagenomic samples can be downloaded from here. 
 Download, unzip, and place the `data` folder inside `metagenomics-workshop-main` folder.
 
 ## 3. Install Docker
 Skip this step if you already have Docker installed on your system.
-Instruction to install Docker is available at [https://docs.docker.com/desktop].
+Instruction to install Docker is available at https://docs.docker.com/desktop.
 
 <!---
 ### Platform-Specific Requirements

going-beyond.md

@@ -1,4 +1,5 @@
 # Going beyond
+Under Construction. 
 
 ## Assembly-based analysis workflows
 

kraken2.ipynb

@@ -5,6 +5,8 @@
    "id": "6a99628a-adb7-444a-bf7a-ebd5808dd814",
    "metadata": {},
    "source": [
+    "# Taxonomic Profiling using Kraken2\n",
+    "\n",
     "There are a number of pre-computed databases here: https://benlangmead.github.io/aws-indexes/k2 . For demonstration purposes, let us use one of the smallest ones : Standard-8. This has already been downloaded in data/kraken2_db/"
    ]
   },

metaphlan.ipynb

@@ -5,6 +5,8 @@
    "id": "29db0336-059d-4e5d-aa87-85c669e06f05",
    "metadata": {},
    "source": [
+    "# Taxonomic Profiling using Metaphlan\n",
+    "\n",
     "Let's use a toy database, since it takes a while to download the entire db. "
    ]
   },