Answers

1. The Pan Genome

Q1: b
Q2: a

2. Preparing the data

Q3: b
Q4: c

3. Performing QC on your data

Q5: If the data is bad going in, the results will be bad coming out.
Q6: Most commonly there is contamination, or the geomes are too fragmented.

4. Running Roary

Q7: c
Q8: b

5. Exploring the results

Q9: b
Q10: c
Q11: c

6. Visualising the results with phandango

Q12: lytN
Q13: No (it is only present in sample 1 and 2)