Congratulations! You have completed all of the tutorials for the ncov workflow. Read on for some next steps.
Table of Contents
On a web browser:
Sign up for a GitHub account if you do not already have one.
Create a repository from the
Click Use this template.
Give your repository a name. We recommend
my-ncov-analysesand will use that name in the following steps.
Click Create repository from template.
In a command prompt:
Go to the
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
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
sequences.fasta files accordingly.
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:
custom_datainput filenames from
idaho.sequences.fastato 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
idahoto your own. Note the name restrictions.
Reword the output dataset title to your own.
Rename the subsampling scheme from
idaho_schemeto your own. Note the name restrictions.
For each sample, increase the
max_sequencesto your own.
usa_contextsample and update the
Now that you have created your own analysis directory, this must be modified, e.g.
Learn more about genomic epidemiology:
Watch this 1-hour video overview by Heather Blankenship on how to deploy Nextstrain for a Public Health lab.