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Discussion Starter #1 (Edited)
Since this is one of the most frequently raised issues on here, let's try to gather the information about diagnostics in one post. If anything in this post is missing or incorrect, please let me know and I will update this post, so we have everything in one place. Maybe PM me so we can keep it tidy.

Disclaimer
Everything that is written below is my best effort at capturing the knowledge and opinions of those on this forum. I own a VAS5054, first-generation OBDeleven with Pro licence and handheld VAG scan tool; for those details I write from experience, for everything else I am reliant on the wisdom of others.

About VW diagnostics
Diagnostics in VW cars are significantly more advanced than the generic OBDII standard. More than just fault codes and reading some values, you can test and configure each of the tens of control modules in the car. The engine, the instrument cluster, the radio, each window - they all have their own individual control module.

A note: if you're new to diagnostics, throw away all your assumptions
The electrical system is not just an electrical system. It is an electronics system. Be under no illusion: there is no switch in the car that directly controls anything. Each switch sends a signal to a control module that decides what to do with it. Your accelerator (gas) pedal is just another electronic input. Even the switches for the overhead lights are just sending a signal to Central Electrics to say "switch the lights on". Some switches connect to one control module, which then tells another control module to do something. The simplest example of this is the window switches: when you press the window switch for the passenger window, the driver's door control module sends a message to the passenger window to lower.

Another note: don't be scared - be methodical
Equipped with the ability to tweak everything, it is tempting to try something "for the sake of trying something". With the right diagnostic tool, you have the ability to measure what is going on, record it, and compare results. Measuring the right things will guide you towards investigating the right area and get you to a simple result. If you are used to investigating things mechanically, you will have to get used to the fact that your investigations have to start with a simple diagnostic check. Many people get frustrated when they take the car to the dealer and the first thing they do is charge you to plug the car into their computer. Now you will have that computer and see what they do.

What you can do with the right tool
  • Fault memory: read the detailed fault memory of each control module with a VAG fault code, generic OBD fault code where applicable and description of the fault, including whether the fault is static or intermittent. For some control modules you will get additional information about the number of times the fault happened, the mileage at which it last happened, and other information
  • Measuring blocks: take measurements from the various sensors attached to the control module and see live data - engine RPM, turbo boost, wheel rotation speed, battery voltage, state of the roof, and so on.
  • Output tests: each control module has a sequence of output tests that will step through and allow you to check that things are working properly. For example, the central electrics module will step through switching on each individual light in turn.
  • Basic settings: these are for checking the correct installation of parts, allowing you to make mechanical changes to ensure that the output is in the correct range. These are where there is one correct value or range (as compared to Adaptation/Coding/Long Coding which are configuration according to preference or equipment level). For example, you can run a test that will allow you to check that your turbocharger boost valve is working correctly - it will rev the engine up, then alternate the boost valve between fully on and fully off so that you can see that the boost is within the correct range.
  • Adaptation: allows you to set some preferences that are not user-accessible. For example, the central electrics module uses adaptation to configure the fade duration on cornering lights. Some comfort settings can also be configured in Adaptation.
  • Coding and Long Coding: these allow you to perform advanced configuration, most of which is only required when changing installed equipment levels. The less advanced control modules (e.g. door control modules) use primitive Coding; more advanced modules like Central Electrics and the radio use Long Coding. You need coding to do things like configure the radio and gateway correctly after installing an amplifier; configure any new control module when replacing a defective part; and perform advanced customisations like configure the lighting setup (enabling/disabling DRLs; adjusting brightness and so on).
  • Guided Fault Finding: only available with "official" tools, Guided Fault Finding will walk you through the steps of diagnosing faults found on your car, automatically performing tests where possible. It will also guide you through manual tests of components (e.g. if your engine gets overboost, it will walk you through testing the resistance of the MAF sensor to ensure that the sensor is working correctly; the software knows the required resistance values).
  • Guided Functions: only available with "official" tools, Guided Functions allow you to perform certain emergency actions (like emergency opening and closing of the roof under fault conditions) step by step.
Your options
  • Cheap generic OBDII code readers, scan tools or dongles with apps - these are next to useless. Any dongle that claims compatibility with something like Torque will not be VW specific. If you have a generic tool, it will tell you some information about the engine, and nothing else. It will not do any of the things listed in "What you can do with the right tool" because it is not the right tool.
  • Handheld VAG-specific scanners - these come at varying price points with different capabilities.
    • At the lower end, tools like the VAG505 Mini can talk to individual control modules. They will do everything except Long Coding, and will not have the ability to make graphs or anything. For basic Coding there is no guidance so you would need to know what you are doing.
    • More expensive tools like the Foxwell NT500 can do everything including Long Coding, and will also log graphs. I don't know whether they have guidance for the Coding and Long Coding settings.
  • VCDS - long established as the "gold standard" of VW diagnostic tools, VCDS connects to a PC, can do everything including Long Coding, and has a lot of helpers that assist with diagnosis and configuration. It will log and export graphs and tables of live data as well as full system scans that serve as a backup for when you want to tweak coding. For Coding and Long Coding, VCDS will tell you what each configuration bit does, making it very easy to perform coding operations.
  • OBDeleven- a new alternative to VCDS. The original OBDeleven dongle requires an Android phone or tablet with internet connection, and can do everything VCDS can do. Information about Coding and Long Coding is provided in a similar way to VCDS, but is user-curated and so is not up to the standard of VCDS. OBDeleven allows you to create and save live graphs and export data traces.
    • A second-generation OBDeleven dongle is now on the market, along with an iPhone app. iPhone functionality is not as complete as Android, but is only missing "Coding II" and trouble code freeze frames, so now there's no need to get an Android phone in case there's something missing. The second-generation dongle also has different tiers (Pro, Ultimate) which allow access to different functionality. For now, the original dongle with a Pro licence will let you do everything. If you have a Pro licence from the original OBDeleven dongle, it will work on the second-generation one; similarly, your Android login will transfer to the iPhone app.
  • VAS5054/VAS6124 with ODIS - the VAS5054 is the original tool that your dealer will use, and ODIS is the Windows software that they will run to talk to it. The original is very expensive but clones are available. This is the only tool that will give you access to Guided Fault Finding and Guided Functions, and the only tool that will allow you to conduct emergency opening and closing of the roof driven by the roof pump in a safe manner (it is possible to perform the emergency actions in VCDS but very dangerous to your roof as it does not perform the checks that ODIS does). Measuring Blocks, Basic Settings and Output Tests are present. Coding and Long Coding is basically unusable as you don't get any of the help that VCDS and OBDeleven provide.
  • Various more expensive options (multi-make with VAG functionality; dealer-level tools and similar) - these usually more expensive than all the other options put together. Unless you have several cars of different makes or are a professional mechanic working in an all-make garage, these are probably not of interest to you. But if you have experience of these, please contribute.
Summary
  • Stay away from generic OBDII readers.
  • You should invest in either VCDS or OBDeleven if you need to diagnose a fault, want to install or replace any part of the electronics, or want to tweak the configuration. A VAG-specific Foxwell tool is likely a suitable alternative.
  • If your roof goes wrong, there are some situations where only a VAS5054 can help you - but it should not be the only tool you own or the first tool you buy.
  • If you want a simple tool for your glovebox that will diagnose issues when you're out without the need for an internet connection, consider a cheap handheld reader - or, if you went for the Foxwell option, keep that in your glovebox.
 

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Excellent! I can add that OBDII diagnostics at its base level describes most of the cheap tools. European car makers were forced by E.U rules and standards to use a common set of fault codes and data standards (protocol) and share them with third parties to make tools widely available. However, they were allowed to retain rights over 'proprietary' codes, commands and technology which were seen as manufacturer or workshop specific. That's where the V.W EOS roof sits. Anybody producing a higher level diagnostics tool hasn't just asked V.W to give them their proprietary codes - they have to test, reverse engineer and analyse to discover them.

Most modern vehicles are full of electronic modules talking to each other. These modules can have 'similar' part numbers but contain different internal softwares and higher level code readers need to be compatible through these module changes and updates. The diagnostics tool manufacturer has to have a continually evolving database capable of recognising modules new, old or changed. Reading back generic (non EOS roof) fault codes is easy but may give a meaningless number and you have to search the internet for more information. This can be very general and not specific to your car.

To cover the huge range of different electronic modules in cars, helper notes and information data specific to that module is required, particularly when the tool is 'adapting' or modifying the software code inside it. The tool has to know exactly what it is because most will not warn you of a code change on an incompatible module. Ever flashed a new phone ROM and bricked it? Cars can be bricked too!

If a tool reads V.W special fault codes for the EOS roof and does a lot more, it will either need data specific to each car module stored locally on a pc, tablet or phone, or access to data on a server run by the tool manufacturer. That's what OBDEleven does. VCDS uses regular 'updates' of it's main application program. These don't change the way it works (clunky) but append new data. If you bought an older EOS and never replaced an electronic module with a newer part, older versions of vcds are fine if you ignore their update nag. Most handheld scanners will read back the generic fault codes and are truly portable with a small display. Their business model can provide enhanced functions through paid for over air updates. Most products now have the possibility for subscription at various feature levels and time limit if you don't renew.

Somebody has to maintain the tool data for evolving newer vehicles and those costs plus profit are either a one off initial high price or you 'rent' the service for less but can't use the tool without it or it 'times out'. Independent garages may use the same diagnostic tool on many different cars, models, years and updated parts. They will pay a high rental contract price for this online access service. This essential connection to a maintained datasource enables a tiered business model to be sold. For DIY diagnostics on one brand (V.W) you don't need this. Diagnostics tools don't actually fix faults for you and may report a module fault caused by something else. You have to learn what they do and their shortcomings.
 

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Discussion Starter #3
Having just got my hands on the second-generation OBDeleven dongle and tested it out briefly with my iPhone, I've updated the top post to reflect that the iPhone version of the OBDeleven app now has all critical features present, so is a good option for those with Apple devices (OBDeleven also works on the iPad). The iPhone app is slightly different to the Android app but overall is pretty similar and just as easy to use.

Performance of the dongle, in terms of time taken to connect and scan, is much better with the second-generation dongle on my iPhone than the first-generation dongle on an Android phone.
 
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