In the Guppy suite, demultiplexing can be performed by one of the two executables, guppy_barcoder and guppy_basecaller.
1. guppy_barcoder allows demultiplexing to be performed on existing fastq files generated by basecalling.
The example command below shows the minimum required parameters:
guppy_barcoder --input_path <folder containing FASTQ and/or FASTA files> --save_path <output folder> --barcode_kits SQK-RBK004
2. guppy_basecaller enables demultiplexing during the basecalling process and so requires fast5 files as the input. An example command is shown below.
guppy_basecaller --input_path <folder containing .fast5 files> --save_path <output folder> --config dna_r9.4.1_450bps_fast.cfg --barcode_kits SQK-RBK004
For more information on both executables and optional parameters, please refer to the Barcoding/demultiplexing section of the Guppy protocol.
MinKNOW can be used to demultiplex barcoded reads during and after sequencing with a point and click interface.