Get tutorial dataset

We will download the tutorial dataset for SARS-Cov2 provided by nextstrain. First, enter your workdir:

cd ~/workdir/

Then clone the repository:

git clone https://github.com/nextstrain/ncov.git

The data is contained in the directory:

ls -l ~/workdir/ncov/data/

total 1724
-rwxrwxr-x 1 ubuntu ubuntu  171914 Nov 19 09:26 example_metadata.tsv
-rwxrwxr-x 1 ubuntu ubuntu 1589835 Nov 19 09:26 example_sequences.fasta.gz

There is a fasta file and a metadata file containing information about each sequence.

Extract the data fasta file, located in the repository:

gunzip ~/workdir/ncov/data/example_sequences.fasta.gz

In the next step, we run the nextstrain basic workflow.

Inspect the data files with less or more:

less ~/workdir/ncov/data/example_sequences.fasta

and:

less ~/workdir/ncov/data/example_metadata.tsv

… to get an impression of what data needs to be provided for nextstrain.

References

Nextstrain SARS Cov2 Tutorial https://nextstrain.github.io/ncov/