The demultiplexing pipeline can be found under "Utilities" in the "Run analysis" page.

Demultiplex

The demultiplex subworkflow is designed to separate multiplexed sequencing data stored in a fastq file into separate files based on a barcoding scheme.

This pipeline is essentially a wrapper around the Ultraplex tool where an input samplesheet is processed for input into Ultraplex. Single or paired-end input is accepted as is support for .csv or .xlsx files.

Inputs

samplesheet

Input .csv. or .xlsx file detailing each sample to be demultiplexed with its 5' and 3' barcoding scheme. The table must be in the following format:

On Flow

To run the pipeline on Flow you simply provide your multiplexed fastq and accompanying excel spreadsheet annotation, then behind the scenes the above samplesheet is populated for you.

Note that samples are created during the demultiplexing pipeline, this is why it's important to fill out the annotation spreadsheet as best you can, so that your samples are generated with accurate metadata.