Take a look at `sox`

   Quoting `man sox`:

    SoX - Sound eXchange, the Swiss Army knife of audio manipulation

    SoX is a command-line audio processing  tool,  particularly  suited  to
    making  quick,  simple  edits  and to batch processing.  If you need an
    interactive, graphical audio editor, use audacity(1).

So, it should be a nice fit as a companion command line alternative to audaciy!


Regarding the actual task of cleaning recordings, take a look at the filter `noisered` for which equals the [noise reduction filter Audacity](http://wiki.audacityteam.org/wiki/Noise_Reduction):

`man sox | less -p 'noisered \['`

       noisered [profile-file [amount]]
               Reduce noise in the audio signal by profiling and filtering.
               This effect is moderately effective at  removing  consistent
               background  noise such as hiss or hum.  To use it, first run
               SoX with the noiseprof effect on a  section  of  audio  that
               ideally  would  contain silence but in fact contains noise -
               such sections are typically found at the  beginning  or  the
               end  of  a recording.  noiseprof will write out a noise pro‐
               file to profile-file, or to stdout if no profile-file or  if
               `-' is given.  E.g.
                  sox speech.wav -n trim 0 1.5 noiseprof speech.noise-profil
               To  actually remove the noise, run SoX again, this time with
               the noisered effect; noisered will reduce noise according to
               a  noise  profile  (which  was generated by noiseprof), from
               profile-file, or from stdin if no profile-file or if `-'  is
               given.  E.g.
                  sox speech.wav cleaned.wav noisered speech.noise-profile 0
               How  much  noise  should be removed is specified by amount-a
               number between 0 and 1 with a default of 0.5.   Higher  num‐
               bers will remove more noise but present a greater likelihood
               of removing wanted components of the audio  signal.   Before
               replacing  an  original  recording with a noise-reduced ver‐
               sion, experiment with different amount values  to  find  the
               optimal one for your audio; use headphones to check that you
               are happy with the results, paying particular  attention  to
               quieter sections of the audio.
               On  most systems, the two stages - profiling and reduction -
               can be combined using a pipe, e.g.
                  sox noisy.wav -n trim 0 1 noiseprof | play noisy.wav noise