I encountered issues when I updated my rooted Nexus 5 from 5.0 to 5.01:

archive does not contain 'boot.sig'
archive does not contain 'recovery.sig'

(You can read about that here: blog post). For the 5.1 update, I decided to manually flash all the files, so as to avoid running into the same errors.

The following is a step by step process of how I updated my rooted Nexus 5.

Notice: If you don’t know how to use adb and fastboot, you should just stop right here. You’ll have to reference another tutorial. For those that proceed, you are responsible for your phone. If you brick it, it’s on YOU!

Prerequisite

• download and install adb & fastboot
• download latest TWRP recovery (openrecovery-twrp-2.8.5.2-hammerhead.img)
• download 5.1 factory image (“hammerhead”)
• download and prep Chainfire’s CF-Auto-Root (XDA link)
• run a Nandroid backup and transfer a copy of the backup to your computer
• (optional) run a full Titanium backup of all your apps and transfer the copies to your computer

Prep of 5.1 factory image

1. expand the hammerhead-lmy47d-factory-6c1ad81e.tgz file
2. expand the image-hammerhead-lmy47d.zip file
3. rename the folder for easier reference (e.g.: extractedZip)
4. move/copy bootloader-hammerhead-hhz12f.img and radio-hammerhead-m8974a-2.0.50.2.25.img files to the extractedZip folder
   • the img files are found in the expanded tgz file from step 1

5.1 update via manual flash

1. connect computer to phone via USB and boot phone into bootloader
   • command: adb reboot bootloader
2. install bootloader-hammerhead-hhz12f.img
   • command: fastboot flash bootloader bootloader-hammerhead-hhz12f.img
3. install radio-hammerhead-m8974a-2.0.50.2.25.img
   • command: fastboot flash radio radio-hammerhead-m8974a-2.0.50.2.25.img
4. install system.img
   • command: fastboot flash system system.img
5. install userdata.img
   • command: fastboot flash userdata userdata.img
6. install boot.img
   • command: fastboot flash boot boot.img
7. install recovery.img
   • command: fastboot flash recovery recovery.img
8. delete the cache
   • command: fastboot erase cache
9. from the phone, boot into Recovery
   • background image is of an Android on its back with chest open and red triangle (default system recovery)
10. press Power + Volume Up buttons to enter into Recovery options
    • note: do NOT press and hold the buttons too long, as this will result in booting into the system (the phone), which will not boot… you’ll be stuck with the boot animation
      • if done accidentally, reboot back into bootloader: Volume Up + Volume Down + Power and continue from step 9
11. select Wipe data/factory data reset
12. reboot phone when data wipe is completed
    • booting into a newly installed system will take awhile — be patient!

After installing 5.1 update: Re-root & install custom Recovery

After the update, your phone has a fresh and clean install of Android 5.1… meaning there is no custom recovery, nor root access. However, Bootloader will still be unlocked. The default settings will not have USB Debugging enabled. USB Debugging enables you to run commands from your computer to your phone via USB.

Install TWRP recovery and Chainfire SuperSU:

1. setup the phone with your existing Gmail account
   • recommend setting up as a new device and use Titanium Backup to reinstall your apps
2. setup USB Debugging
3. connect computer to phone via USB and reboot phone into bootloader
4. flash TWRP recovery: openrecovery-twrp-2.8.5.2-hammerhead.img
   • command: fastboot flash recovery openrecovery-twrp-2.8.5.2-hammerhead.img
5. execute Chainfire’s CF-Auto-Root
   • Mac command: ./root-mac.sh
     • on a Mac, this will require the admin password of the Mac computer
   • the background will have a red pirate android
   • when complete, the phone will automatically reboot
6. in Google Play store, update SuperSU to the current version
7. SuperSU requires updating binary
   • select “Normal” and reboot when finished

Reinstall apps & check phone settings

To reinstall apps, download Titanium Backup and restore from there. If you have issues, I would recommend also using Nandroid Manager (Google Play Store Link). I resolved most of my issues by using Nandroid Manager to install the app and Titanium Backup to install the data.

I recommend checking the phone settings. I’m on Ting (MVNO provider on the Sprint network; CDMA), so I updated my PRL and profile. The default for “Preferred network type” is set to Global; I had to update that to LTE.