Connecting Demultiplexing

Demultiplexing is a data generation step similar to instruments that write data. Data is read from Illumina sequencer run directories. Ideally, the ${LZ}-INGESTED “shadow” landing zone directory is readable for the demultiplexing process (as in the reference implementation) but in principle the data can also be retrieved from the ingested data in RODEOS iRODS. Usually, the bcl2fastq2 tool by the vendor Illumina is run in a custom wrapper script. The wrapper script should write a marker file indicating the completion of the demultiplexing process.

The RODEOS Ingest software comes with built-in support for our software package Digestiflow but its implementation is generic and also allows custom demultiplexing scripts with custom marker file names.