The nccopy has options to specify what kind of output to generate and optionally what level of compression to use and how to chunk the output.
nccopy [-k kind] [-u] [-d level] [-s]
[-c chunkspec] [-m n] [-h n] [-e n] input output
[-k kind] kind of output netCDF file
omitted => same compression as input
1 or 'classic' => classic file format
2 or '64-bit-offset' => 64-bit-offset format
3 or 'netCDF-4' => netcdf-4 format
4 or 'netCDF-4 classic model' => netCDF-4 classic model
[-u] convert unlimited dimensions to fixed size in output
[-d level] "deflation" level, uses zlib
omitted => output compressed like input
0 => uncompressed
1 => fast, lowest compression
...
9 => slow, highest compression
[-s] shuffling option, sometimes improves compression
...
input name of input file or OPeNDAP URL
output name of output file