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:

  • Huge species diversity – the tool accepts multiple references and makes multi-genome tables and plots, including Krona charts.
  • Commonly unknown species content – the tool automatically detects and downloads reference sequences from NCBI.
  • Presence of highly relative genomes – the tool detects chimeric contigs and reports “interspecies misassemblies” in addition to the regular assembly errors types.

MetaQUAST can be fed with multiple assemblies, thus is perfect for comparison.

MetaQUAST is distributed within QUAST package since version 2.2: download the latest version, see changelog.

MetaQUAST specific sections in the Manual: running, output description

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