Most of our workflows do support the parallel analysis of demultiplexed data. If a workflow has a sample sheet parameter, then it does supports such barcoded data. To run with multiple barcodes, you should input a directory that contains subdirectories one for each barcode. Optionally a sample sheet can be included to replace barcodes with sample names in any output files.

eg. input directory structure

├── barcode01
│   ├── reads0.fastq
│   ├── reads1.fastq
│   └── reads2.fastq
├── barcode02
│   ├── reads0.fastq
│   ├── reads1.fastq
│   └── reads2.fastq
└── barcode03
    └── reads0.fastq

Sample sheet files should be laid out according to the MinKNOW sample sheet specification. For EPI2ME Labs workflows a file minimally needs the barcode and sample_id fields:

barcode,sample_id
barcode01,sample01
barcode02,sample02
barcode03,sample03