QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST project.
It can works both with and without a given reference genome.
The tool accepts multiple assemblies, thus is suitable for comparison.
More at http://bioinf.spbau.ru/quast
http://bioinformatics.oxfordjournals.org/content/early/2013/03/09/bioinformatics.btt086.long
Comments
You can also try LAZER, it produces the same evaluation as Quast but is 5.6 times faster and use half the memory
http://www.csd.uwo.ca/~ilie/LASER/
Understanding the terms used in QUAST http://quast.bioinf.spbau.ru/manual.html