Include own data

As we have already seen, the data files are located in:

~/workdir/ncov/data/

All you need to do, to include your own data, is append the consensus fasta sequences to the fasta file, and add metadata to the metadata file.

Add fasta sequences

Copy the consensus sequences to the data folder:

cat ~/workdir/results_artic/barcode_0?.fasta > ~/workdir/ncov/data/consensus_sequences.fasta

Then open the sequence file in an editor:

gedit ~/workdir/ncov/data/consensus_sequences.fasta

and give the following short names to the sequences:

Germany/OWL-B0001/2020
Germany/OWL-B0002/2020
Germany/OWL-B0003/2020
Germany/OWL-B0004/2020
Germany/OWL-B0005/2020

Attention: Please use exactly the names above, since these are the names, we provide in the metadata file below.

Then append the fasta file to the example sequences with (maybe inspect it with less or more before):

cat  ~/workdir/ncov/data/consensus_sequences.fasta >> ~/workdir/ncov/data/example_sequences.fasta

Add metadata

Download the metadata for our samples:

cd ~/workdir/ncov/
wget https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/coursedata2020/metadata.tsv

Append it to the example metadata file:

cat ~/workdir/ncov/metadata.tsv >> ~/workdir/ncov/data/example_metadata.tsv

Rerun analysis

Then make sure, the nextstrain environment is active. If not:

conda activate nextstrain

Run the basic nextstrain workflow with:

cd ~/workdir/ncov/
snakemake --cores 14 --profile ./my_profiles/getting_started

Then start the auspice server:

cd ~/workdir/ncov
nextstrain view auspice/

View the results in a browser with:

firefox http://127.0.0.1:4000

That’s it for the short nextstrain tutorial, you can check out the official nextstrain site for many more things you can do with nextstrain, which is way beyond the scope of this workshop.

References

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