A Quality Assessment Tool for Genome Assemblies by the Center for Algorithmic Biotechnology.
QUAST evaluates genome assemblies by computing various metrics, including
- N50, length for which the collection of all contigs of that length or longer covers at least 50% of assembly length
- NG50, where length of the reference genome is being covered
- NA50 and NGA50, where aligned blocks instead of contigs are taken
- Misassemblies, misassembled and unaligned contigs or contigs bases
- Genes and operons covered
The QUAST MultiQC module parses the
report.tsv files generated by
QUAST and adds key metrics to the report General Statistics table.
All statistics for all samples are saved to
By default, the QUAST module is configured to work with large de-novo genomes, showing thousands of contigs, mega-base pairs and other sensible defaults.
If these aren’t appropriate for your genomes, you can configure them as follows:
quast_config: contig_length_multiplier: 0.001 contig_length_suffix: "Kbp" total_length_multiplier: 0.000001 total_length_suffix: "Mbp" total_number_contigs_multiplier: 0.001 total_number_contigs_suffix: "K"
The default module values are shown above. See the main MultiQC documentation for more information about how to configure MultiQC.
The QUAST module will also parse output from
MetaQUAST runs (
combined_reference/report.tsv file is parsed, and folders
not_aligned are ignored.
If you want to run MultiQC against auxiliary MetaQUAST runs, you must explicitly pass these files to MultiQC:
Note that you can pass as many file paths to MultiQC as you like
and use glob expansion (eg.
File search patterns
quast: fn: report.tsv shared: true