Commit dae0d302 authored by Sam Nooij's avatar Sam Nooij
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Add content list

parent d61c2a8c
......@@ -12,6 +12,22 @@ An automated pipeline for screening trimmed reads and assembled scaffolds from [
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## 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)
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## Pipeline description
This pipeline uses the table with classified scaffolds, trimmed reads and assembled (filtered) scaffolds to look for species and sequences of interest.
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