I have paired-end reads (Illumina HiSeq) from a metagenome in two Fastq files. These non-overlapping reads (the exact lengths of gaps are not known) have already been quality checked, and I want to concatenate them into one file. I was thinking of using Fastq Joiner, but I have a doubt... When sequencing paired ends with Illumina HiSeq 2500, the R2 sequences will be in reverse direction respect to their R1, right? When I use Fastq Joiner, what it does is simply glue the 2 seqs together, as they are (without reversing the R2) and with no sign for the internal gap (eg. and N). Does this make sense? Do I need to do a reverse complement of my R2 reads?