I have HiSeq paired-end run data for an assay using our own dual barcodes to ID specific samples that I need to demultiplex before sample specific analysis.
I'm having trouble finding a tool for the job. The person who used to do this would basically use a single barcode demultiplexing software and run multiple times, but it seems a little messy to me.
I've tried to write my own tool, which works but feels pretty slow. I'm just using my own computer, so I have no idea how long this kind of process usually takes / if people generally do this on a dedicated machine / cluster.
I think I'm being unclear. I have samples that have already demultiplexed by the illumina machine by index. When designing our PCR primers, the actual primers were preceded by a golay or hamming barcode. The combination of forward and reverse primer barcode uniquely identifies a sample name and assay
So, I need to demultiplex based on the first 12 or 8 nt from the 5' end of each paired-end read.