Add content list

README.md

@@ -12,6 +12,22 @@ An automated pipeline for screening trimmed reads and assembled scaffolds from [
 
 ---
 
+## Content
+
+- [Pipeline description](#pipeline-description)
+- [Requirements](#requirements)
+- [User manual](#user-manual)
+  - [1. Preparing data](#1-preparing-data)
+    - [Importing from Jovian](#importing-from-jovian)
+    - [Choosing a reference](#choosing-a-reference)
+    - [Install snakemake](#make-sure-you-have-snakemake-installed)
+  - [2. Running the pipeline](#2-running-the-pipeline)
+- [Project organisation](#project-organisation)
+- [Licence](#licence)
+- [Citation](#citation)
+
+---
+
 ## Pipeline description
 
 This pipeline uses the table with classified scaffolds, trimmed reads and assembled (filtered) scaffolds to look for species and sequences of interest.