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While you can go with the links approach, suggested by Gyan in the comments. You could also generate a list of files that you want to use for encoding, and then use -f concat. I have tried it with the following: find . -name '*.jpeg' -exec echo "file '"{}"'" >> list.text \; ffmpeg -f concat -r 25 -safe 0 -i list.text -c:v libtheora ...

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