Both stacks and uneak are made for single end reads. If you have paired end data here is a little cheat that puts “fake” barcodes onto the mate pairs and prints them all out to one file. It also adds the corresponding fake quality scores.
perl GBS_fastq_RE-multiplexer_v1.pl BarcodeFile R1.fastq R2.fastq Re-barcoded.fastq
BarcodeFile should look like (same as for my demultiplexing script) spaces must be tabs:
# note this could also look like this:
As it does not actually use the names (it just looks at the second column).
Here it is: