Mr Nobody

I'm having another problem with doing a differential analysis of RNA sequences using command line Bio bioinformatics. I have been given 5 case and 5 control reads when need to be compared

I need to identify an organism using results generated from Illumina sequencing but I have no idea where to start. I know that I need to check my results quality and then make an assembly but I don't know where to begin... PS, I'm new to the whole command line Bioinformatics thing