I have read a few papers, some of them used GenMark, or PacBios proprietary Iso-Seq pipeline but as I'm just a Bachelor's student I am having trouble understanding how exactly it works.

Can some one roughly explain the steps of a state of the art pipeline that I could apply to an invertebrate?

The data of my cnidarian species should be annotated with help of PacBio RNA seq data.

Your insights are much appreciated!