I am not very experienced with sequencing, so maybe there might be a simple solution to the following problem. We ran a sequencing run on an Illumina NextSeq this week with 75 cycles and dual indices. The original plan was to load 12 different library samples, each barcoded individually with a single 8 nt barcode and then demultiplex using bcl2fastq. This approach has worked before. This time, during setup of the run we chose dual indexed sequencing by accident and noticed when we tried demultiplexing using bcl2fastq. At the moment I demultiplexed without using a sample-sheet, so I have a large fastq file containing undetermined reads. Is there any way to demultiplex a dual indexed sequencing run when only a single barcode per sample was used? Any ideas using a script would also be very welcome, programming is no problem for me.