Possible to use Segger J-Link with Intel Quartus to flash FPGA?
AFAIK not directly, but through OpenOCD.
You can use quartus_cpf to convert the programming file to SVF format, and then set up the J-Link in OpenOCD.
I have a similar setup even for my USB Blaster, because I can program from a machine that doesn't have QuartusII installed that way (also it allows me to avoid the libudev0-shim hack to allow Quartus's jtagd to find the device).
My build script generates the SVF with
quartus_cpf \
    --convert \
    --frequency=10MHz \
    --voltage=3.3V \
    --operation=p \
    output_files/pcie_test.sof \
    output_files/pcie_test.svf

and I send it to the device with
openocd \
    -f /usr/share/openocd/scripts/interface/altera-usb-blaster.cfg \
    -c init \
    -c 'svf pcie_test.svf' \
    -c exit

You would probably use one of the j-link scripts for the initial setup. If you have more devices on the same scan chain, either build a CDF file in the QuartusII Programmer and pass that to quartus_cpf, or tell it the sum of the IR lengths before and after your device.
For details on QuartusII command line tools, see the scripting reference.