MetaQUAST evaluates and compares metagenome assemblies based on alignments to close references. It is based on QUAST genome quality assessment tool, but addresses features specific for metagenome datasets:
 
MetaQUAST can be fed with multiple assemblies, thus is perfect for comparison.
 
MetaQUAST is distributed within QUAST package since version 2.2.

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MetaQUAST specific sections in the Manual: running, output description

Citation:

Alla Mikheenko, Vladislav Saveliev, Alexey Gurevich,
MetaQUAST: evaluation of metagenome assemblies,
Bioinformatics (2016) 32 (7): 1088-1090. doi: 10.1093/bioinformatics/btv697
First published online: November 26, 2015

Citation of other formats
 

Examples of comparison of 4 assemblers on 3 datasets generated with MetaQUAST v3.2:

CAMI simulated toy dataset      MetaHIT real dataset     HMP real dataset
 

Please help us to make MetaQUAST better by sending your comments, bug reports, and suggestions to quast.support@bioinf.spbau.ru