QUAST

Description

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 multiqc_data/multiqc_quast.txt.

Configuration

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.

MetaQUAST

The QUAST module will also parse output from MetaQUAST runs (metaquast.py).

The combined_reference/report.tsv file is parsed, and folders runs_per_reference and not_aligned are ignored.

If you want to run MultiQC against auxiliary MetaQUAST runs, you must explicitly pass these files to MultiQC:

multiqc runs_per_reference/reference_1/report.tsv

Note that you can pass as many file paths to MultiQC as you like and use glob expansion (eg. runs_per_reference/*/report.tsv).

File search patterns

quast:
  fn: report.tsv
  contents: "Assembly\t"
  num_lines: 2