Handling NGS data using IGV

[Alarrisa]

Good evening,

I do not work in bioinformatics, I have chosen a module in bioinformatics and completely out of my depth!
I have an assessment where I am given a reference bacterial genome in FastA format and a GFF file containing the annotations and the position of predicted genes.
I have illumine sequence reads generated by shotgun sequencing of genomes of several closely related bacteria.
The objective: identify interesting differences among the sequenced bacterial genomes!
I have no idea how to interpret this data. I started the module late due to personal reasons and I have 2 weeks to submit a poster with my findings!!

Can one or a few of you bioinformatics wizards help me out please?

[GenoMax]

Can you tell us what you have learned as a part of this module? Do you know what the raw data looks like? What needs to be done with it in terms of QC/clean-up? Do you know what sequence alignment is with reference to NGS data? Are you limited to certain tools? Are you allowed to use online tools?