[galaxy-user] joining two FASTq files with overlap reads

I have a data generated from Miseq 2X250 bp these reads are overlap, before aligning to a my custom bacterial genome, I have to join these two mate pair Fastq files and then use BWA alignment tool. I am aware of COPE/ FLASH can be used. I am looking for if there are similar tool or any way I can join two Fastq files which i can use for alignment. Just to clarify further with overlapping reads as such BWA is not aligning the reads. I have used both as mate pair or used only forward reads to align to genome. The idea is to find SNPs in different samples. Thanks Kanwar