The Tutorial Data Set

As you have started the VM with a volume attached, this volume needs to be given to the ubuntu user for easy access:

sudo chown ubuntu:ubuntu /mnt/

Create a link in your home directory to the mounted volume:

cd
ln -s /mnt/ workdir

The tutorial dataset is located in our object store. We have also prepared some precomputed results.You can get both here:

cd ~/workdir
wget https://s3.bi.denbi.de/cmg/mgcourses/longread2025/Data.tar.gz
wget https://s3.bi.denbi.de/cmg/mgcourses/longread2025/Results.tar.gz

Then, unpack the tar archive:

tar -xzvf Data.tar.gz
tar -xzvf Results.tar.gz

and remove the tar archives:

rm Data.tar.gz
rm Results.tar.gz

Have a short look, on what is contained within the data directory:

ls -l ~/workdir/data/
-rw-r--r-- 1 ubuntu ubuntu   6849457 Aug 30  2019 Reference.fna
drwxr-xr-x 2 ubuntu ubuntu     20480 Aug 30  2019 fast5
drwxrwxr-x 2 ubuntu ubuntu      4096 Sep  5  2019 fast5_small
drwxrwxr-x 2 ubuntu ubuntu      4096 Sep 12  2019 fast5_tiny
drwxr-xr-x 2 ubuntu ubuntu      4096 Aug 30  2019 illumina
-rw-rw-r-- 1 ubuntu ubuntu 117496419 Jun 24 10:28 pb_cov_20.fq.gz
-rw-rw-r-- 1 ubuntu ubuntu 293425053 Jun 24 10:27 pb_cov_50.fq.gz

There are three folders with Nanopore fast5 data, a Reference genome for later comparison, some illumina data and simulated PacBio data.

If you want to disable system beep sounds:

xset -b