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 output_kind] [-d level] [-s] [-c chunkspec]
[-u] [-m n] [-h n] [-e n] input output
[-k output_kind] kind of output netCDF file
omitted => same 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
[-d level] deflation level, from 1 (faster but lower compression)
to 9 (slower but more compression)
[-s] shuffling option, sometimes improves compression
[-c chunkspec] specify chunking for dimensions, e.g. "dim1/N1,dim2/N2,..."
[-u] convert unlimited dimensions to fixed size in output
[-m n] memory buffer size (default 5 Mbytes)
[-h n] set size in bytes of chunk_cache for chunked variables
[-e n] set number of elements that chunk_cache can hold
input name of input file or OPeNDAP URL
output name of output file