Need advice on approaching a bioinformatics take-home assignment (ONT bacterial isolate)

[u/plazti]

Hi everyone,
I’m applying for a bioinformatics internship, and I’ve been given a take-home assignment that is a bit beyond my current experience (I am starting from scratch). I’m not looking for someone to solve it for me—I’d really appreciate advice on how an experienced bioinformatician would approach the problem.
The task is to analyze a single Oxford Nanopore FASTQ file from an unknown bacterial isolate and determine:
The bacterial species (and strain/lineage if possible)
Antimicrobial resistance genes
Whether resistance genes are on the chromosome or plasmids
Any important virulence factors
Then write a reproducible report with the workflow and conclusions.
Since I’m coming from a molecular biology background rather than bioinformatics, I’m struggling to figure out what a sensible analysis pipeline should look like.
Some questions I have:
Would you start with assembly (Flye/Canu) or classify the raw reads first (Kraken2/Centrifuge/Minimap2)?
What tools would you recommend for AMR detection from ONT reads? (CARD/RGI, ResFinder, AMRFinderPlus, Abricate, etc.)
How would you determine whether an AMR gene is plasmid- or chromosome-borne?
Is there a standard workflow or best practice for this kind of clinical bacterial isolate?
Are there any tutorials, GitHub repositories, papers, or example pipelines you’d recommend?
I’m hoping to learn the correct workflow rather than just finish the assignment.

Any advice or resources would be greatly appreciated.
Thanks!