I am relatively new to bioinformatics world, therefore having some issues to construct a workflow that would suit my needs. Hence, I would kindly ask for your opinion and advice. I have Illumina shotgun sequences of 5 metagenomes. I would like to end up with functional profile of all 5 samples that can be comparable. In addition, I would like to calculate taxa contribution for few genes of my interest. What would be the best approach to achieve that? Is it the right way to do the assembly and binning? Perhaps just assembly? Or use the un-assembled reads?