I had 57,206 contigs from the Velvet assembler, with an N50 of 15,957. I got an assembly size of 348,942,280 bp (without any Ns).
When I fed these contigs into SSPACE, the N50 improved to 30,443, but my assembly size decreased to 348,541,909 bp, despite the inclusion of 31,358 Ns.
I used the same paired-end data for scaffolding with SSPACE, that I had initially used to build the contigs with Velvet.
How did the size of my assembly reduce?