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:
Sign up for a GitHub account if you do not already have one.
Create a repository from the
ncov-tutorial
template repository:Click Use this template.
Give your repository a name. We recommend
my-ncov-analyses
and will use that name in the following steps.Click Create repository from template.
In a command prompt:
Go to the
ncov/
directory.Clone your new repository, replacing
<username>
with your own username:git clone https://github.com/<username>/my-ncov-analyses
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:
Change the
custom_data
input filenames fromidaho.metadata.tsv
andidaho.sequences.fasta
to your own.Change the regional input dataset from North America to an appropriate region for your custom focal data. See the complete list of available URLs.
Rename the output dataset from
idaho
to your own. Note the name restrictions.Reword the output dataset title to your own.
Rename the subsampling scheme from
idaho_scheme
to your own. Note the name restrictions.For each sample, increase the
max_sequences
to your own.Rename the
usa_context
sample and update thequery
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.