I wanted to learn bioinformatics and I'm doing week 4 of the FastTrack Bioinformatics 2025 course, but I'm stuck in the exercises of that week. I need some hints.

The exercise has 3 papers. Ebola, Zika, Staphylococcus. I chose to do the Zika one: https://www.ncbi.nlm.nih.gov/pubmed/26952870

I read the paper from top to bottom and looked at the supplementary materials, but I think I'm not understanding the data retrieval questions of the exercises. It is asking:

• Identify the accession numbers for the genome referenced in your assigned paper.
• Write shell commands to download the genome and annotation data. Ensure your commands are reusable and reproducible.

I identified the accession number to be: GSE78711 which leads me to BioProject PRJNA313294 and SRA SRP070895. But none of these are accession numbers for genome references.

As I understand it, the paper explains that they infected human cells with the Zika virus and then sequenced the infected human cells. I tried to look everywhere, but I'm not seeing a Zika reference genome associated with this paper. Did I miss it? From what I have learned so far a reference genome will be a .fna/.fa file whereas annotations will be gff3 files. So I moved forward a few weeks to view what future exercises entail because sometimes looking forward can give one understanding of the ask, but they all build upon this exercise. Future questions ask to align the viral/bacterial genome in the paper to the reference genome in the paper.

Do I just have to download any Zika virus reference genome I find in NCBI? I found various, but none of them are connected to the paper and I don't understand if the questions just want me to do that. To download any Zika reference genome so that in future exercises I align the SRA associated .fastq files to whichever Zika virus reference genome I decided to get. Because as far as I know, I cannot align Zika virus sequence reads to the human genome reference. They are different organisms. I may be misunderstanding the questions.