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InfluxDB
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First thing I use is qvs, this one can take the mkv files apart (demux) and get you workable files(I recommend the mkvextract option). It also can transcode the video, and has a whole bunch of other encoding features I haven't figured out yet. After you get the video out I would recommend encoding it at 8-bit, CRF 17.0, slower/veryslow and either the film or grain preset depending on how grainy the original video is. Qvs can also do x265 which is more efficient at encoding, but I'm not sure what the recommended settings for relatively lossless for that one are. Qvs also has limited re-assembling features (remuxing), but for remuxing you're probably better off using mkvtoolnix. After you re-encode the video just add them into mkvtoolnix as source files, set the output and start multiplexing it, it will put the video back together.