There is no transformation as you named it, there is a wrapping though. This wrapping is performed by a tool called Apache Cordova, formerly known as PhoneGap.
Other similar instruments exist, I refer to Ionic as the one using AngularJS, which happens to match with my preference among the many available JS frameworks out there.
By just using HTML5, as your research assistant suggests, you will not build an hybrid application, but a web application: the assistant is trying to remove a layer from the technology stack you picked, in my humble opinion as a consequence of your lack of understanding, in order to make your life easier.
If I were you I would listen to the guy, but keeping an eye to Ionic, getting back as soon as you will have finished your thesis: ionic is great!
If you want to be smart and show the guy you are better than he thinks, you can build both solutions with limited effort, but first focus on the one he is pointing you toward: he is on the handle side of the sword!
To build both solutions what you will have to do is ensure to build your web app (HTML5) so that all interactions with the database occur through RESTful services.
Building the plain HTML5 application you can still use the Ionic CSS and JS models to create the web application UI, but you will not be able to use any of the Apache Cordova plugins and your usage of the Ionic CLI tool must be wise.
If you do so, converting the plain web app into an hybrid app will be a matter of running a couple of Ionic CLI commands.