Dear Colin,
thank you for the fast reply. Actually, the barcodes are not part of the read sequences.
I have two separate barcodes files I1 and I2. And R1 and R2 for the reads.
From this post (Importing multiplexed paired-end data with separated barcode sequence files - #11 by ebolyen). I found the suggestion to use the old script extract_barcodes.py
This worked out, now I have forward.fastq, reverse.fastq and barcodes.py