README.md

BiRC-Thyme: Project in Bioinformatics

This repository contains all code used during the Project in Bioinformatics I did as part of my MSc in Bioinformatics at Aarhus University.

The main objective of this project was to explore the use Homology-Scaffolding to obtain a Chromosome-level assembly of Thymus vulgaris.

Slides of my PiB presentation

You can find the slides of my presentation here (GitHub Pages).

Run the pipeline

This project is managed using snakemake and makes use of Conda and Singularity to run the different parts of the project in isolated environments. Scripts intended to be run interactively are located in the analysis/ directory.

To run the whole pipeline, follow the steps below:

Set up

Install snakemake and Mamba using conda:

conda create -c conda-forge -c bioconda -n snakemake snakemake mamba

Activate the enviroment and check all programs are installed:

conda activate snakemake
snakemake -v && mamba -V && singularity version

Run the following line to make sure you have all the necessary input files:

snakemake check -c1

We will rely on conda or container environments to run the pipeline to execute the different steps. Use the -n option to see a dry-run (what will be done without running it if any of the files are not up to date)

snakemake -n --use-conda --use-singularity

And add the maximum number of cores allowed when you want to run it:

snakemake -c10 --use-conda --use-singularity

Project structure

We distinguish between source files (input directory), external data, and work results. See the corresponding README file for each directory for more information.