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  • cumulative contigs length,
  • all kinds of N-metrics,
  • genes and operons covered,
  • GC content.



Both QUAST 3.2 and QUAST 4.0 do accept the same arguments and so the following tutorial should be applicable to both the versions. QUAST-4.0 has Icarus visualizer for denovo assembly evaluation inaddition to other feature in 3.2

Report Example


  1. A CyVerse account. (Register for an CyVerse account here -
  2. Inputs 
    1. Input file (Genome assemblies generated by using any of the genome assemblers in fasta format)
  3. Output
    1. Output directory name
  4. Options
    1. FASTA file with the reference genome sequence (Users can select a genome from the list of available genome or they can upload their custom genome in zipped format)
    2. Genes (File with gene positions in reference)
    3. Operons (See manual for file formats)
    4. Skip contigs shorter than (default is 500bp)
  5. Advanced options
    1. Caption (This will enter in your report. Number of labels should match the number of files)
    2. Find genes (Enables gene finding. Affects performance)
    3. Scaffolds (The assemblies are scaffolds and not contigs)
    4. eukaryotic (find genes with GeneMark-ES) (Genome is eukaryotic. Affects gene finding and contig alignment. Default is prokaryotic (GeneMarkS is used for gene finding))