This demo includes a selection of EV-D68 sequences - full-genome. Or are they? They should be, for this run!
Can you create a Nextstrain workflow Snakefile that will do everything needed to make a Nextstrain build?
Clone this directory to your local computer so you can start playing with the files. Ask Emma if you need help cloning.
Use the Zika tutorial Snakefile as a starting point! Create your own Snakefile in the directory, and start to fill it in based on the Zika Snakefile.
Hint: Add files and rules to the Snakefile one by one as you go, so you can more easily spot mistakes!
You'll need to add a reference sequence to align and then to label where genes start and end. Have a look at the reference sequence used by the Zika tutorial and note the type of file it is. A .gb (Genbank) file.
There are official reference sequences stored by NCBI. For EV-D68, we often use the earliest known sequence, called 'Fermon'.
In particular, note that the filter step can take a list of sequences to be excluded. Are there some that look questionable, that you should remove from the build? Are there other attributes you might want to filter sequences by - date, or sequence length? Don't forget you can always type augur filter to see what options are available.
You should have a quick look at intermediate files (if you can) as you go, but also carefully look at your final build. How does it compare to the official EV-D68 build? (It will be smaller - but otherwise?) You might need to change things and run again :)
The config/auspice_config_zika.json is copied from the Zika Tutorial - so it may not be ideal for EV-D68! How can you change it so that it fits better to the virus, and can you adjust how it displays?
Once you have a built a fairly good tree, we can try to annotate it with clades - chat with Emma!