Illumina sequencing instruments have onboard control and workflow software. This software includes a robust data-streaming component, which acts as a software broker with the BaseSpace Sequence Hub API. Through this broker, you can transfer individual base call (*.bcl) files over an encrypted connection to the BaseSpace Sequence Hub. You can then verify the files and assemble them into samples for analysis on the interface. You can perform this transmission and analysis during the sequencing of a run.
The instrument control software does not allow publicly addressable inbound communications. All communication is made through standard https requests initiated by the user at the instrument. Each data-upload transaction is linked to an authenticated user account.