Once you have some sequence, you'll want to map it to some reference. 100M reads that are 50 bases long each really aren't gonna help anybody until you put them in context. There are lots of mappers out there. Some are easier to use than others, and for the most part, any one of them will get the job done.
Taejoon Kwon did a nice test of how the different mappers performed on X. laevis, which is important because of the pseudogenomes can confuse mappers sometimes. He found that RNA-STAR is probably the best, but the commands to run it are very clunky (see below).