It seems that I am missing something, so I will just describe my problem.
I have paired-end illumina reads in fastq format. In .txt I have the sequence for forward and reverse primers and tags for each experiment. I will attach an example file. The read has following format: tag-primer-fragment
I need to demultiplex the reads according to the experiment and get rid of the adapters, primers, experiment sequences. There are two scripts that could do that in
split_libraries_fastq.py - but I do not have The barcode read fastq files
demultiplex_fasta.py - it operates only on fasta format but I do not want to loose the quality information as in further I might want to filter according to the quality.
Is there any other way I could demultiplex without losing quality information?