make.contigs with index reads?

I am trying to demultiplex a MiSeq run in which I used paired-end dual barcodes. So, I have 4 files, forward and reverse reads plus forward and reverse index reads. I’d like to use the new functionality of make.contigs to process these, but I notice that make.contigs seems to be looking for 2 files, not 4. Am I missing something?

I would talk with your sequencing people to get the MiSeq to do the demultiplexing. There’s really no need to get back the index reads. When we run our machine we’re able to set the output to be multiplexed so that you get a fastq file for the forward and reverse reads for each sample. To do this you need to set up your sample sheets - this can also be done offline by your sequencing facility.