Download the latest version of CyanogenMod 13 from Official CyanogenMod website https://download.cyanogenmod.org/?device=mako. I would recommend Stable release only. Make sure to download system image (CyanogenMod Build), recovery image (CyanogenMod Recovery) and Google App from https://wiki.cyanogenmod.org/w/Google_Apps.
1. You will need Android SDK platform tool and we will be using fastboot and adb.
2. Now boot the phone in recovery mode, hold down Volume Down + Power button until bootloader appears, then navigate to Bootloader by clicking volume up/down and select by clicking Power button.
3. Open terminal and then navigate to folder where you have placed Android SDK platform tools. Type
sudo ./fastboot oem unlock if your OEM is locked else
sudo ./fastboot oem lock
sudo ./fastboot oem unlock
4. Now lets erase some partitions like recovery, system, boot, cache and userdata.
sudo ./fastboot erase recovery
sudo ./fastboot erase system
sudo ./fastboot erase boot
sudo ./fastboot erase cache
sudo ./fastboot erase userdata
5. Now lets flash recovery image
sudo ./fastboot flash recovery cm13xxx-recovery.img
6. Now reboot the phone to Recovery Mode like you did in step 2.
7. Now select Wipe/Factory Reset and also any wipe option available.
8. So let flash in System Image and Google Apps using adb sideload. Select Apply Update in the recovery mode, and select ABD Sideload
sudo ./abd sideload CM13xxx.zip
sudo ./abd sideload open-gappxxx.zip
9. Now select Reboot System from the recovery mode menu. At first time boot it will take some time, just relax and wait for it to boot.
Now your Nexus 4 will boot in CyanogenMod 13 in turn Android 6.0.1