Next steps

Congratulations! You have completed all of the tutorials for the ncov workflow. Read on for some next steps.

Create your own analysis directory

On a web browser:

1. Sign up for a GitHub account if you do not already have one.

2. Create a repository from the ncov-tutorial template repository:

   1. Go to https://github.com/nextstrain/ncov-tutorial.

   2. Click Use this template.

   3. Give your repository a name. We recommend my-ncov-analyses and will use that name in the following steps.

   4. Click Create repository from template.

In a command prompt:

1. Go to the ncov/ directory.

2. Clone your new repository, replacing <username> with your own username:

   git clone https://github.com/<username>/my-ncov-analyses
   

3. Read the next section to learn how to modify genomic-surveillance.yaml.

Modify the genomic surveillance workflow configuration

Instead of an Idaho-focused workflow config, you can provide your own data for the custom_data input. Follow the same steps in the tutorial for GISAID download but select your own set of sequences and rename your metadata.tsv and sequences.fasta files accordingly.

Note

Workflow run time increases with the number of sequences, and the GISAID web interface has a maximum of 5,000 sequences per download.

Then, use the following steps to customize names, titles, and context:

1. Change the custom_data input filenames from idaho.metadata.tsv and idaho.sequences.fasta to your own.

2. Change the regional input dataset from North America to an appropriate region for your custom focal data. See the complete list of available URLs.

3. Rename the output dataset from idaho to your own. Note the name restrictions.

4. Reword the output dataset title to your own.

5. Rename the subsampling scheme from idaho_scheme to your own. Note the name restrictions.

6. For each sample, increase the max_sequences to your own.

7. Rename the usa_context sample and update the query accordingly.

Warning

File paths in the config files must start with the analysis directory. For example, in the tutorial:

auspice_config: ncov-tutorial/auspice-config-custom-data.json

Now that you have created your own analysis directory, this must be modified, e.g.

auspice_config: my-ncov-analyses/auspice-config-custom-data.json

Additional resources

• Learn more about genomic epidemiology:

  • An applied genomic epidemiological handbook by Allison Black and Gytis Dudas

  • Genomic Epidemiology Seminar Series by Chan Zuckerberg Initiative Genomic Epidemiology (CZ GEN EPI)

  • COVID-19 Genomic Epidemiology Toolkit by Centers for Disease Control and Prevention (CDC)

• Review all possible options to configure your SARS-CoV-2 analyses with Nextstrain.

• Watch this 1-hour video overview by Heather Blankenship on how to deploy Nextstrain for a Public Health lab.