I'm also involved in the project. Ideally we'd like it to be able to be used both as both a microscope and as a sequencer. Potentially there are other uses too. For example this paper uses a customised Illumina GAIIx sequencer to do high throughput measurement of on and off rates: https://www.pnas.org/content/114/21/5461 While this does involve sequencing with Illumina reagents, my point is that it's possible to use customised flow cells and reagents for new assays that you might dream up. Software to run such assays could be built on top of what we are doing.

I have heard that the BGISEQ-500 (https://www.bgi.com/resources/sequencing-platforms) is a similar machine...

Our initial focus is on writing the device adapters that enable Micro-Manager (https://micro-manager.org) to talk to the HiSeq hardware. MM will then be able to drive it like a microscope as well as providing access to all the other fluidics switches, pumps, sensors etc. The MM user interface is extensible and plugins can be written to support assays such as sequencing. MM also exposes all of the devices and functionality in a scripting environment.