Hi schulpen, against what genome do you want to align the reads, before the assembly?

If you are working on de novo assembly, you want to assemble the reads, not map. \ Mapping will align the reads with an already assembled genome (generally your reference genome). \ De novo assembly will take your reads and generate a new assembly without any knowledge of your reference (if one exists). In this case you will want to decide on the appropriate assembler for your species which is pretty hard to do, unless some bench-marking has already been done with your species.