Guides / Apps for encoding

I have started encoding, but have now gotten to making videos where multiple video streams need to be combined from a bluray source, into one video file - Does anyone know any programs for this, or any in depth guides on Remuxing / etc?

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ffmpeg, if you need a gui use handbreak
- I currently use Handbrake (I'm not much without a GUI aha) but it doesn't seem to have any options for merging / combining video files. I'm hoping to encode here, but the bluray source splits the movie into a couple of video files, and I'd like to combine them first before encoding
  
  Are you trying to concat streams or just to remux? For remuxing as roawre said there’s also MkvToolNix, which works great (and it has a gui don’t worry)
With ffmpeg

ffmpeg -i src -c copy -map 0:v:0 -map 0:v:1 -map 0:a out.mkv
ffmpeg uses a sectioned parameter approach. Input parameters and input, optionally multiple, output parameters and output target.
In my example I specified copy as codec so the streams are copied as-is, without reencoding. I used map to map video streams 1 and 2 of the first input, and default/all audio streams.
The ffmpeg reference docs are thorough. The wiki has some more guide, example, and explanatory docs.
Mkvtoolnix ?
mkvtoolnix to create a remux then encode that remux
As a follow up, thankyou to everyone for your help! MKVToolNix is fantastic, and does it all - question answered, thanks again!

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