JTAG chain debugger tools scripts & JTAG clock management

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I then would like to apply stimuli on DUT inputs via the JTAG chain and to read outputs too.

I found the JTAG chain debugger tool in Quartus which would allow me to read and write data via JTAG on DUT I/Os.

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A higher-level of abstraction already exists to perform this type of testing. I've created a tutorial that walks you through the basics:

http://www.alterawiki.com/wiki/using_the_usb-blaster_as_an_sopc/qsys_avalon-mm_master_tutorial

Cheers,

Dave