Already paired input?

We are working with fastq files that contain already paired reads. This is for a class and the files in the SRA were joined ~250bp fastq. How can we use those for input to Mothur, specifically make.contigs()? Thank you!!!

This question seems to be the same as what was just answered here (if this link works within the forum): Processing MiSeq single (unpaired) reads

Thanks dwaite, we will also try your suggestion!

If they pairs have already been assembled, you can skip make.contigs and go straight into quality filtering ( + trim.seqs).