As mentionned during the presentation, for the parctical course you need to assemble a genome and control it's quality.
First, we're going to install the necessary tools.
For this, we can use "conda" which is an environment manager that facilitates the installation of tools

1- creation of the environment
conda create -n flye

2- activate the env
conda activate flye

3- install the tools
conda install flye
conda install bioconda::quast
conda install -c bioconda nanoplot

For busco we're going to need another environment, because we have dependencies conflicts between the tools

1- creation of the environment
conda create -n busco

2- activate the env
conda activate busco 

3- install busco
conda install -c conda-forge -c bioconda busco=5.8.2


Once all the tools are installed, we can run the tools

1- activate the env 
conda activate flye

2- running the tools
	-Quality control
		NanoPlot --fastq {fastq_file} -o nanopolot_output
	- Assembly
		flye --nano-raw {fastq_file} --out-dir flye_output --genome-size 5m
	- Assessment of the assembly
		quast {assembly.fasta} -o quast_results

		busco -i {assembly.fasta} -m genome -l bacteria_odb12 -o busco_output