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QUAST

note

Quality assessment tool for genome assemblies.

http://quast.bioinf.spbau.ru/

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