Recap Day 2 / Preparations Day 3

We have performed an assembly on the ARTIC dataset and since it didn’t work well we did another using a WGS dataset which we also polished using racon and medaka.

Today, we are working with the ARTIC datasets again. Please go to your data_artic directory, and download all datasets, untar and remove the tar files:

cd ~/workdir/data_artic/

for i in {1..5}
do
wget https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/coursedata2020/basecall_0$i.tar.gz
tar -xzvf basecall_0$i.tar.gz
rm basecall_0$i.tar.gz
done

We also have some Illumina data fitting to our samples:

for i in {1..5}
do
wget https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/coursedata2020/Illumina_0$i.tar.gz
tar -xzvf Illumina_0$i.tar.gz
rm Illumina_0$i.tar.gz
done