shnsplit is a utility for splitting audio files based on a cue sheet provided by the utility
The shnsplit and cuebreakpoints utilities can be installed with the following:
# apt-get install cuetools shntool flac
To split a FLAC file
audio.flac into separate tracks using
cuesheet.cue, run the following:
$ cuebreakpoints cuesheet.cue | shnsplit -o flac audio.flac
The split tracks will be placed in the current directory.
You can split other files like WAV as well as FLAC, and even transcode WAV to FLAC while splitting.