QUAST now supports evaluation of metagenomic assemblies. The tool accepts multiple references, and produces several reports:
— for all contigs and all input genomes merged into one,
— separate reports for only contigs aligned to a particular genome,
— for the contigs not aligned to any reference provided.
metaquast.py contigs_1 contigs_2 ... -R reference_1,reference_2,reference_3,...
All other options for metaquast.py are the same as for quast.py.
In addition, MetaGeneMark is used for finding genes in metagenomic assemblies. In metaquast.py by default, in quast.py with --meta option.
Other changes include a new option --labels (or -l) for providing human-readable assembly names. Those names will be used in reports, plots and logs, instead of file names. For example:
If your labels include spaces, use quotes:
-l SPAdes,"Assembly 2",Assembly3
-l "SPAdes 2.5, SPAdes 2.4, IDBA-UD"
A one more important change: in place of --allow-ambiguity, a new option
-a) introduced; it lets specify a particular way to process ambiguous regions: -a one, -a all or -a none.
We also fixed some bugs in misassemblies detection algorithm.
You can download QUAST 2.2 here.