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QUAST 2.2 released

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.

Usage: contigs_1 contigs_2 ... -R reference_1,reference_2,reference_3,...
All other options for are the same as for
In addition, MetaGeneMark is used for finding genes in metagenomic assemblies. In by default, in 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:

   -l SPAdes,IDBA-UD

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 --ambiguity-usage (-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.