Update Nexus 5 From KK 4.4.4 to M 6
You can flash directly to Marshmallow using the 6.0.1 (MMB29K) factory image. Follow the flashing instructions, which includes unlocking your bootloader.

I highly recommend then installing a custom recovery such as TWRP using the fastboot method. Having the custom recovery will enable you to flash other zip updates like SuperSU to get permanent root.

Note that Google's flash-all process replaces your custom recovery with the stock recovery, so make sure to reflash whatever custom recovery you choose right after. You can avoid this by flashing each partition manually instead of using flash-all.