Copying data and preparing the directories

First let’s create a directory named `wgs_assembly` for this practical. And then, under that directory create subdirectories to hold our data and results:

mkdir ~/wgs_assembly
mkdir -p ~/wgs_assembly/data
mkdir -p ~/wgs_assembly/results
mkdir -p ~/wgs_assembly/results/qc
mkdir -p ~/wgs_assembly/results/short_long_reads_assembly

Now, copy the data into our data directory:

cp -r /home/mtb_upm/mtb_genomics_workshop_data/genome-assembly-annotation/data/* ~/wgs_assembly/data

Define variables for convenience:

MYDATADIR=~/wgs_assembly/data
MYRESULTSDIR=~/wgs_assembly/results