This program demultiplexes fastq data having “in-line” barcodes, based on a given list of barcodes and a barcode start position. It tries to assign each fastq record to the most likely barcode, taking into account the sequence qualities (interpreted as being sanger-encoded).
It was developed to handle iCLIP data generated in the MHE unit.
It is available in the tars cluster (
module load qaf_demux), and has a Galaxy wrapper.
Its source code is available here: https://gitlab.pasteur.fr/bli/qaf_demux.