This paper on Neisseria gonorrhoeae in South Africa uses a reference mapping approach to build the phylogeny used in Figure 1.
The challenge for this homework is to fetch the reference sequence used in the paper, fetch at least some of the samples in the Bioproject PRJNA575338 and build a phylogeny. Breaking this down:
What is the reference sequence used in this project?
How can you download this reference genome in Genbank format?
How many sequences are there in the PRJNA575338 Bioproject?
How can you download these sequence reads?
How can you build a sample sheet for this dataset?
What would the Bactopia command line for analysing this dataset using snippy look like?
Final challenge: can you run Bactopia and get the expected results with this dataset?